Publication: Difference between revisions

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== 2024 ==
== 2025 ==
<ol>
<ol>
<li value="249"> {{Paper
<li value="270"> {{Paper
|title=DeepSLICEM: Clustering CryoEM particles using deep image and similarity graph representations
|title=The CAGE complex: a hollow, megadalton, protein assembly in prokaryotic and eukaryotic microbes
|authors=Palukuri MV, Marcotte EM
|authors=McCafferty CL, Hoogerbrugge G, Papoulas O, Schwartz EA, Ritchey S, Taylor DW, Brilot AF, Marcotte EM
|journal=bioRxiv
|journal=bioRxiv
|pub_year=2024
|pub_year=2025
|volume=Deposited Feb 8
|page=
|page=
|link=https://doi.org/10.1101/2024.02.04.578778
|volume=Sept 22
|pubmed=38370702
|link=https://doi.org/10.1101/2025.09.22.677704
}}
|pubmed=
<li value="248"> {{Paper
|title=Label-free proteomic comparison reveals ciliary and non- ciliary phenotypes of IFT-A mutants
|authors=Leggere J, Hibbard J, Papoulas O, Lee C, Pearson CG, Marcotte EM, Wallingford JB
|journal=Molecular Biology of the Cell
|pub_year=2024
|volume=Jan 3
|page=mbcE23030084
|link=https://doi.org/10.1091/mbc.E23-03-0084
|comment=[https://www.biorxiv.org/content/10.1101/2023.03.08.531778v1 bioRxiv preprint] (deposited Mar 9, 2023)
|pubmed=38170584
}}
}}
</li>
</li>
</ol>
<li value="269"> {{Paper
== 2023 ==
|title=Identification of Aspartyl-tRNA Synthetase as Co-purifying with Wheat Germ eIF2
<ol>
|authors=Papoulas O, Marcotte EM, Browning KS
<li value="247"> {{Paper
|journal=MicroPubl Biol
|title=SARS-COV-2 Omicron variants conformationally escape a rare quaternary antibody binding mode
|pub_year=2025
|authors=Goike J, Hsieh CL, Horton AP, Gardner EC, Zhou L, Bartzoka F, Wang N, Javanmardi K, Herbert A, Abbassi S, Xie X, Xia H, Shi PY, Renberg R, Segall-Shapiro TH, Terrace CI, Wu W, Shroff R, Byrom M, Ellington AD, Marcotte EM, Musser JM, Kuchipudi SV, Kapur V, Georgiou G, Weaver SC, Dye JM, Boutz DR, McLellan JS, Gollihar JD
|journal=Communications Biology
|pub_year=2023
|page=1250
|volume=6(1)
|link=https://doi.org/10.1038/s42003-023-05649-6
|pubmed=38082099
|pdf=CommunicationsBiology_OmicronAntibody_2023.pdf
}}
<li value="246"> {{Paper
|title=Robust and scalable single-molecule protein sequencing with fluorosequencing
|authors=Mapes JH, Stover J, Stout HD, Folsom TM, Babcock E, Loudwig S, Martin C, Austin MJ, Tu F, Howdieshell CJ, Simpson ZB, Blom T, Weaver D, Winkler D, Vander Velden K, Ossareh PM, Beierle JM, Somekh T, Bardo AM, Anslyn EV, Marcotte EM, Swaminathan J
|journal=bioRxiv
|pub_year=2023
|page=
|page=
|volume=Deposited Sept 16
|volume=Jul 9
|link=https://doi.org/10.1101/2023.09.15.558007
|link=https://doi.org/10.17912/micropub.biology.001594
|pubmed=37745461
|pubmed=40756276
}}
<li value="245"> {{Paper
|title=Systematic Profiling of Ale Yeast Protein Dynamics across Fermentation and Repitching
|authors=Garge RK, Geck RC, Armstrong JO, Dunn B, Boutz DR, Battenhouse A, Leutert M, Dang V, Jiang P, Kwiatkowski D, Peiser T, McElroy H, Marcotte EM, Dunham MJ
|journal=G3
|pub_year=2023
|page=jkad293
|volume=
|link=https://doi.org/10.1093/g3journal/jkad293
|comment=[https://doi.org/10.1101/2023.09.21.558736 bioRxiv preprint] (deposited Sept 22, 2023)
|pubmed=38135291
}}
}}
<li value="244"> {{Paper
</li>
|title=Mining Patents with Large Language Models Demonstrates Congruence of Functional Labels and Chemical Structures
<li value="268"> {{Paper
|authors=Kosonocky CW, Wilke CO, Marcotte EM, Ellington AD
|title=Comparative Proteomic Profiling of Receptor Kinase Signaling Reveals Key Trafficking Components Enforcing Plant Stomatal Development
|journal=arXiv
|authors=Bai P, Vu MH, Komatsu C, Papoulas O, Ebine K, Nozawa A, Sawasaki T, Ueda T, Marcotte EM, Torii KU
|pub_year=2023
|journal=bioRxiv
|pub_year=2025
|page=
|page=
|volume=Deposited Sept 15
|volume=Deposited July 23
|link=https://arxiv.org/abs/2309.08765
|link=https://doi.org/10.1101/2025.07.20.665823
|pubmed=
|pubmed=
}}
}}
<li value="243"> {{Paper
</li>
|title=Estimating error rates for single molecule protein sequencing experiments
<li value="267"> {{Paper
|authors=Smith MB, VanderVelden K, Blom T, Stout HD, Mapes JH, Folsom TM, Martin C, Bardo AM, Marcotte EM  
|title=Protein Abundance Inference via Expectation Maximization in Fluorosequencing
|journal=bioRxiv  
|authors=Kipen J, Smith MB, Blom T, Zhou SB, Marcotte EM, Jaldén J
|pub_year=2023
|journal=bioRxiv
|pub_year=2025
|page=
|page=
|volume=Deposited July 19
|volume=Deposited July 14
|link=https://doi.org/10.1101/2023.07.18.549591
|link=https://doi.org/10.1101/2025.07.10.664057
|pubmed=37502879
|pubmed=
}}
}}
<li value="242"> {{Paper
</li>
|title=An amino acid-resolution interactome for motile cilia illuminates the structure and function of ciliopathy protein complexes
<li value="266"> {{Paper
|authors=McCafferty CL, Papoulas O, Lee C, Bui KH, Taylor DW, Marcotte EM, Wallingford JB  
|title=Physical and functional interaction of Lrrc56 and Odad3 controls deployment of axonemal dyneins in vertebrate multiciliated cells
|journal=bioRxiv  
|authors=Reyes-Nava NG, Lee C, Papoulas O, Hong J, Marcotte EM, Wallingford JB
|pub_year=2023
|journal=bioRxiv
|pub_year=2025
|page=
|page=
|volume=Deposited July 10
|volume=Deposited June 25
|link=https://doi.org/10.1101/2023.07.09.548259
|link=https://doi.org/10.1101/2025.07.02.662827
|pubmed=37781579
|pubmed=40631331
}}
}}
<li value="241"> {{Paper
</li>
|title=Integrated modeling of the Nexin-dynein regulatory complex reveals its regulatory mechanism
<li value="265"> {{Paper
|authors=Ghanaeian A, Majhi S, McCafferty CL, Nami B, Black CS, Yang SK, Legal T, Papoulas O, Janowska M, Valente-Paterno M, Marcotte EM, Wloga D, Bui KH
|title=VerteBrain reveals novel neural and non-neural protein assemblies conserved across vertebrate evolution
|authors=Dang V, Voigt B, Yang D, Hoogerbrugge G, Lee M, Cox RM, Papoulas O, McWhite CD, Pradeep R, Leggere JC, Gray RS, Marcotte EM
|journal=bioRxiv
|pub_year=2025
|page=
|volume=Deposited May 28
|link=https://doi.org/10.1101/2025.05.26.656196
|pubmed=40501792
}}
</li>
<li value="264"> {{Paper
|title=The human ciliopathy protein RSG1 links the CPLANE complex to transition zone architecture
|authors=Vazquez N, Lee C, Valenzuela I, Phan TP, Derderian C, Chávez M, Mooney NA, Demeter J, Aziz-Zanjani MO, Cusco I, Codina M, Martínez-Gil N, Valverde D, Solarat C, Buel AL, Thauvin-Robinet C, Steichen E, Filges I, Joset P, De Geyter J, Vaidyanathan K, Gardner T, Toriyama M, Marcotte EM, Roberson EC, Jackson PK, Reiter JF, Tizzano EF, Wallingford JB
|journal=Nature Communications
|journal=Nature Communications
|pub_year=2023
|pub_year=2025
|page=5741
|page=5701
|volume=14
|volume=16(1)
|link=https://www.nature.com/articles/s41467-023-41480-7
|link=https://doi.org/10.1038/s41467-025-61005-8
|pubmed=37398254
|comment=[https://doi.org/10.1101/2024.09.25.614984 bioRxiv preprint] (Deposited Sep 26, 2024)
|pdf=NatureCommunications_NDRC_Structure_2023.pdf
|pubmed=39386566
|comment=[https://doi.org/10.1101/2023.05.31.543107 bioRxiv preprint] (deposited June 01, 2023)
}}
}}
<li value="240"> {{Paper
</li>
|title=Distinctive interactomes of RNA polymerase II phosphorylation during different stages of transcription
<li value="263"> {{Paper
|authors=Moreno RY, Juetten KJ, Panina SB, Butalewicz JP, Floyd BM, Ramani MKV, Marcotte EM, Brodbelt JS, Zhang Yan
|title=Heritable symbiont producing nonribosomal peptide confers extreme heat sensitivity and antifungal protection on its host
|journal=iScience
|authors=Maeda GP, Dang V, Kelly MK, Sundar A, Arnott R, Marcotte EM, Moran NA
|pub_year=2023
|journal=Proc Natl Acad Sci U S A
|page=107581
|pub_year=2025
|pdf=SSRN-id4449188.pdf
|page=e2509873122
|volume=26(9)
|volume=122(26)  
|link=https://ssrn.com/abstract=4449188
|pubmed=40569380
|comment=[https://papers.ssrn.com/sol3/papers.cfm?abstract_id=4449188&download=yes&redirectFrom=true SSRN preprint] (deposited May 17, 2023)
|link=https://doi.org/10.1073/pnas.2509873122
|pubmed=37664589
}}
}}
</li>
</li>
<li value="239"> {{Paper
<li value="262"> {{Paper
|title=Native doublet microtubules from Tetrahymena thermophila reveal the importance of outer junction proteins
|title=Structure and organization of full-length Epidermal Growth Factor Receptor in extracellular vesicles by cryo-electron tomography
|authors=Kubo S, Black CS, Joachimiak E, Yang SK, Legal T, Peri K, Khalifa AAZ, Ghanaeian A, McCafferty CL, Valente-Paterno M, De Bellis C, Huynh PM, Fan Z, Marcotte EM, Wloga D, Bui KH
|authors=Gonzalez-Magaldi M, Gullapalli A, Papoulas O, Liu C, Leung AY-H, Guo L, Brilot A, Marcotte EM, Ke Z, Leahy DJ
|journal=Nature Communications
|journal=Proc Natl Acad Sci U S A
|pub_year=2023
|pub_year=2025
|volume=14
|page=e2424678122
|page=Article number: 2168
|volume=122(23)
|link=https://www.nature.com/articles/s41467-023-37868-0
|link=https://doi.org/10.1073/pnas.2424678122
|pubmed=37061538
|comment=[https://doi.org/10.1101/2024.11.25.625301 bioRxiv preprint] (Deposited Nov 28, 2024)
|pdf=NatureCommunications_MTDoubletStructure_2023.pdf
|pubmed=40455995
}}
}}
</li>
</li>
<li value="238"> {{Paper
<li value="261"> {{Paper
|title=Does AlphaFold2 model proteins' intracellular conformations? An experimental test using cross-linking mass spectrometry of endogenous ciliary proteins
|title=Moving towards sequencing-based metabolomics
|authors=McCafferty CL, Pennington EL, Papoulas O, Taylor DW, Marcotte EM
|authors=Clark-ElSayed A, Ellington AD, Marcotte EM
|journal=Communications Biology
|journal=Trends in Genetics
|pub_year=2023
|pub_year=2025
|volume=6
|link=https://doi.org/10.1016/j.tig.2025.04.006
|page=Article number: 421
|page=554-555
|link=https://www.nature.com/articles/s42003-023-04773-7
|volume=41(7)
|pdf=CommunicationsBiology_XLTestOfAF2_2023.pdf
|pubmed=40335328
|pubmed=37061613
}}
|comment=[https://doi.org/10.1101/2022.08.25.505345 bioRxiv preprint] (deposited Aug 26, 2022)
</li>
<li value="260"> {{Paper
|title=Plastic degradation by enzymes from uncultured deep sea microorganisms
|authors=Acosta DJ, Barth DR, Bondy J, Appler KE, De Anda V, Ngo PHT, Alper HS, Baker BJ, Marcotte EM, Ellington AD
|journal=ISME Journal
|pub_year=2025
|link=
|page=
|volume=
}}
}}
<li value="237"> {{Paper
</li>
|title=Protein nonadditive expression and solubility contribute to heterosis in ''Arabidopsis'' hybrids and allotetraploids
<li value="259"> {{Paper
|authors=June V, Xu D, Papoulas O, Boutz D, Marcotte EM, Chen ZJ
|title=After 75 Years, an Alternative to Edman Degradation: A Mechanistic and Efficiency Study of a Base-Induced Method for N‑Terminal Peptide Sequencing
|journal=Frontiers in Plant Science
|authors=Deol H, Raeisbahrami A, Ngo PHT, Swaminathan J, Papoulas O, Marcotte EM, Anslyn EV
|pub_year=2023
|journal=Journal of the American Chemical Society
|volume=14
|pub_year=2025
|page=1252564
|link=https://doi.org/10.1021/jacs.5c03385
|link=https://doi.org/10.3389/fpls.2023.1252564
|pubmed=40226999
|pubmed=37780492
|page=13973-13982
|pdf=FrontiersInPlantScience_ProteinAggregation_2023.pdf
|volume=147(16)  
|comment=[https://doi.org/10.1101/2023.03.01.530688 bioRxiv preprint] (deposited Mar 2, 2023)
}}
}}
</li>
</li>
</ol>
<li value="258"> {{Paper
 
|title=Serendipity and the slime mold: a visual survey of megadalton protein assemblies reveals the structure of the polyketide synthase Pks16
== 2022 ==
|authors=Hoogerbrugge G, Keatinge-Clay AT, Marcotte EM
<ol>
<li value="236"> {{Paper
|title=Humanized CB1R and CB2R yeast biosensors enable facile screening of cannabinoid compounds
|authors=Mulvihill CJ, Lutgens J, Gollihar JD, Bachanová P, Marcotte EM, Ellington AD, Gardner EC
|journal=bioRxiv
|journal=bioRxiv
|pub_year=2022
|pub_year=2025
|volume=Deposited Oct 12
|link=https://doi.org/10.1101/2025.03.12.642832
|page=
|page=
|link=https://doi.org/10.1101/2022.10.12.511978
|volume=Deposited Mar 12
}}
</li>
<li value="257"> {{Paper
|title=A protein complex in the extreme distal tip of vertebrate motile cilia controls their organization, length, and function
|authors=Hong J, Lee C, Madhu G, Papoulas O, Atayeter E, Hoogerbrugge G, Pan J, Takagishi M, Manzi N, Dickinson DJ, Horani A, Brody SL, Marcotte EM, Prakash VN, Park TJ, Wallingford JB
|journal=bioRxiv
|pub_year=2025
|page=
|volume=Deposited Feb 19
|link=https://doi.org/10.1101/2025.02.19.639145
|pubmed=40027778
}}
</li>
<li value="256"> {{Paper
|title=Progress toward a comprehensive brain protein interactome
|authors=Dang V, Voigt B, Marcotte EM
|journal=Biochemical Society Transactions
|pub_year=2025
|page=303–314
|pdf=BiochemSocTrans_BrainInteractome_2025.pdf
|volume=53(1)
|link=https://doi.org/10.1042/BST20241135
|pubmed=39936389
}}
</li>
<li value="255"> {{Paper
|title=Combinatorial phosphorylation on CTD of RNA polymerase II selectively controls transcription and export of protein-coding mRNAs
|authors=Panina SB, Irani S, Hardtke HA, Stephenson R, Floyd BM, Moreno RY, Marcotte EM, Zhang Q, Zhang YJ
|journal=bioRxiv
|pub_year=2025
|page=
|volume=Deposited Jan 15
|link=https://doi.org/10.1101/2025.01.13.632769
|pubmed=
|pubmed=
}}
}}
<li value="235"> {{Paper
</li>
|title=Amino acid sequence assignment from single molecule peptide sequencing data using a two-stage classifier
</ol>
|authors=Smith MB, Simpson ZB, Marcotte EM
 
|journal=PLoS Computational Biology
== 2024 ==
|pub_year=2023
<ol>
|volume=19(5)
<li value="254"> {{Paper
|page=e1011157
|title=Thr4 phosphorylation on RNA Pol II occurs at early transcription regulating 3'-end processing
|comment=[https://doi.org/10.1101/2022.09.23.509260 bioRxiv preprint] (deposited Sept 26, 2022)
|authors=Moreno RY, Panina SB, Irani S, Hardtke HA, Richardson R, Floyd BM, Marcotte EM, Zhang Q, Zhang YJ
|link=https://doi.org/10.1371/journal.pcbi.1011157
|journal=Science Advances
|pubmed=37253025
|pdf=ScienceAdvances_CTDThr4Phosphorylation_2024.pdf
|pdf=PLoSComputationalBiology_Whatprot_2023.pdf
|pub_year=2024
|volume=10(36)
|page=eadq0350
|pubmed=39241064
|link=https://doi.org/10.1126/sciadv.adq0350
}}
}}
<li value="234"> {{Paper
</li>
<li value="253"> {{Paper
|title=Alternative proteoforms and proteoform-dependent assemblies in humans and plants
|title=Alternative proteoforms and proteoform-dependent assemblies in humans and plants
|authors=McWhite CD, Sae-Lee W, Yuan Y, Mallam A, Gort-Frietas NA, Ramundo S, Onishi M, Marcotte EM
|authors=McWhite CD, Sae-Lee W, Yuan Y, Mallam AL, Gort-Frietas NA, Ramundo S, Onishi M, Marcotte EM
|journal=Molecular Systems Biology
|pdf=MolecularSystemsBiology_MappingProteoforms_2024.pdf
|pub_year=2024
|volume=20
|page=933-951
|link=https://doi.org/10.1038/s44320-024-00048-3
|comment=[https://doi.org/10.1101/2022.09.21.508930 bioRxiv preprint] (Deposited Sept 22, 2022)
|pubmed=38918600
}}
</li>
<li value="252"> {{Paper
|title=Ancient eukaryotic protein interactions illuminate modern genetic traits and disorders
|authors=Cox RM, Papoulas O, Shril S, Lee C, Gardner T, Battenhouse AM, Lee M, Drew K, McWhite CD, Yang D, Leggere JC, Durand D, Hildebrandt F, Wallingford JB, Marcotte EM  
|journal=bioRxiv
|journal=bioRxiv
|pub_year=2022
|pub_year=2024
|volume=Deposited Sept 22
|page=
|page=
|link=https://doi.org/10.1101/2022.09.21.508930
|volume=Deposited May 29
|pubmed=
|link=https://doi.org/10.1101/2024.05.26.595818
|pubmed=38853926
}}
}}
<li value="233"> {{Paper
</li>
|title=The protein organization of a red blood cell
<li value="251"> {{Paper
|authors=Sae-Lee W, McCafferty CL, Verbeke EJ, Havugimana PC, Papoulas O, McWhite CD, Houser JR, Vanuytsel K, Murphy G, Drew K, Emili A, Taylor DW, Marcotte EM
|title=An amino acid-resolution interactome for motile cilia illuminates the structure and function of ciliopathy protein complexes
|journal=Cell Reports
|authors=McCafferty CL, Papoulas O, Lee C, Bui KH, Taylor DW, Marcotte EM, Wallingford JB
|pub_year=2022
|journal=Developmental Cell
|volume=40(3)
|pdf=DevelopmentalCell_CiliaryInteractome_2024.pdf
|page=111103
|pub_year=2025 (online 2024)
|pdf=CellReports_RBCs_2022.pdf
|page=1–14
|link=https://doi.org/10.1016/j.celrep.2022.111103
|volume=60
|comment=[https://doi.org/10.1101/2021.12.10.472004 bioRxiv preprint] (deposited Dec 11, 2021)
|comment=[https://doi.org/10.1101/2023.07.09.548259 bioRxiv preprint] (deposited July 10, 2023)
|pubmed=35858567
|pubmed=37781579
}}
}}
<li value="232"> {{Paper
</li>
|title=Integrative modeling reveals the molecular architecture of the Intraflagellar Transport A (IFT-A) complex
<li value="250"> {{Paper
|authors=McCafferty CL, Papoulas O, Jordan MA, Hoogerbrugge G, Nichols C, Pigino G, Taylor DW, Wallingford JB, Marcotte EM
|title=Estimating error rates for single-molecule protein sequencing experiments
|journal=eLife
|authors=Smith MB, VanderVelden K, Blom T, Stout HD, Mapes JH, Folsom TM, Martin C, Bardo AM, Marcotte EM  
|pub_year=2022
|journal=PLoS Computational Biology
|page=e81977
|pub_year=2024
|pubmed=36346217
|page=e1012258
|volume=11
|volume=20(7)
|link=https://elifesciences.org/articles/81977
|comment=[https://doi.org/10.1101/2023.07.18.549591 bioRxiv preprint] (deposited July 19, 2023)
|comment=[https://doi.org/10.1101/2022.07.05.498886 bioRxiv preprint] (deposited Jul 5, 2022)
|link=https://doi.org/10.1371/journal.pcbi.1012258
|pdf=eLife_IFTAStructure_2023.pdf
|pubmed=37502879
}}
}}
<li value="231"> {{Paper
</li>
|title=Rapid, scalable, combinatorial genome engineering by Marker-less Enrichment and Recombination of Genetically Engineered loci (MERGE)
<li value="249"> {{Paper
|authors=Abdullah M, Greco BM, Laurent JM, Garge RK, Boutz DR, Vandeloo M, Marcotte EM, Kachroo AH
|title=A Humanized CB1R Yeast Biosensor Enables Facile Screening of Cannabinoid Compounds
|journal=Cell Reports Methods
|authors=Mulvihill CJ, Lutgens J, Gollihar JD, Bachanová P, Tramont C, Marcotte EM, Ellington AD, Gardner EC
|pub_year=2023
|journal=International Journal of Molecular Sciences
|page=100464
|pub_year=2024
|pubmed=37323580
|pdf=IJMS_CB1Ryeast_2024cover.pdf
|volume=3
|volume=25(11)
|pdf=CellReportsMethods_MERGE_2023.pdf
|page=6060
|link=https://doi.org/10.1016/j.crmeth.2023.100464
|link=https://doi.org/10.3390/ijms25116060
|comment=[https://doi.org/10.1101/2022.06.17.496490 bioRxiv preprint] (deposited Jun 21, 2022) [http://www.marcottelab.org/paper-pdfs/CellReportsMethods_MERGE_2023_Supplement.pdf Supplement]
|comment=[https://doi.org/10.1101/2022.10.12.511978 bioRxiv preprint]
|pubmed=38892247
}}
}}
<li value="230"> {{Paper
</li>
|title=Molecular complex detection in protein interaction networks through reinforcement learning
<li value="248"> {{Paper
|authors=Palukuri MV, Patil RS, Marcotte EM
|title=Mining Patents with Large Language Models Demonstrates Congruence of Functional Labels and Chemical Structures
|journal=BMC Bioinformatics
|authors=Kosonocky CW, Wilke CO, Marcotte EM, Ellington AD
|pub_year=2023
|journal=Digital Discovery
|page=306
|pdf=DigitalDiscovery_CheF_2024.pdf
|pubmed=37532987
|pub_year=2024
|volume=24
|page=1150-1159
|link=https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-023-05425-7
|volume=3(6)
|comment=[https://doi.org/10.1101/2022.06.20.496772 bioRxiv preprint] (deposited Jun 21, 2022) [https://rdcu.be/dipi4 pdf available here]
|link=https://doi.org/10.1039/D4DD00011K
|comment=[https://arxiv.org/abs/2309.08765 arXiv preprint] (deposited Sept 15, 2023)
|pubmed=38196747
}}
}}
<li value="229"> {{Paper
</li>
|title=Evaluating the Effect of Dye–Dye Interactions of Xanthene-Based Fluorophores in the Fluorosequencing of Peptides
<li value="247"> {{Paper
|authors=Bachman JL, Wight CD, Bardo AM, Johnson AM, Pavlich CI, Boley AJ, Wagner HR, Swaminathan J, Iverson BL, Marcotte EM, Anslyn EV
|title=Systematic mapping of TF-mediated cell fate changes by a pooled induction coupled with scRNA-seq and multi-omics approaches
|journal=Bioconjugate Chemistry
|authors=Lee M, Guo Q, Kim M, Choi J, Segura A, Genceroglu A, LeBlanc L, Ramirez N, Jang YJ, Jang Y, Lee BK, Marcotte EM, Kim J
|pub_year=2022
|journal=Genome Research
|page=1156-1165
|pub_year=2024
|pubmed=35622964
|volume=34
|volume=33(6)
|page=1–14
|pdf=BioconjugateChemistry_DyeDyeInteractions_2022.pdf
|link=https://doi.org/10.1101/gr.277926.123
|link=https://doi.org/10.1021/acs.bioconjchem.2c00103
|pubmed=38580401
|pdf=GenomeResearch_iTF-seq_2024.pdf
}}
</li>
<li value="246"> {{Paper
|title=What can recent methodological advances help us understand about protein and genome evolution?
|authors=Orengo C, Ehrenreich IM, Marcotte EM, Kolodny R, Ben-Tal N, de Boer CG, McWhite CD, Ranganathan R, Honig B, Bromberg Y, Thornton JW
|journal=Cell Systems
|pub_year=2024
|volume=15(3)
|page=205-210
|link=https://www.sciencedirect.com/science/article/pii/S2405471224000607?dgcid=coauthor
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|authors=Garge RK, Laurent JM, Kachroo AH, Marcotte EM
|title=Protein sequencing, one molecule at a time
|journal=Genetics
|authors=Floyd BM, Marcotte EM
|pub_year=2020
|journal=Annual Review of Biophysics
|volume=215(4)
|pub_year=2022
|pubmed=32522745
|volume=51
|page=1153-1169
|link=https://doi.org/10.1146/annurev-biophys-102121-103615
|pdf=Genetics_HumanizingCytoskeleton_2020.pdf
|page=181-200
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|pubmed=34985940
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<li value="208"> {{Paper
</li>
|title=Humanization of yeast genes with multiple human orthologs reveals principles of functional divergence between paralogs
</ol>
|authors=Laurent J, Garge RK, Teufel AI, Wilke CO, Kachroo AH, Marcotte EM
 
|journal=PLoS Biology
== 2021 ==
|pub_year=2020
<ol>
|volume=18(5)
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|page=e3000627
|title=Studies of Surface Preparation for the Fluorosequencing of Peptides
|pdf=PLoSBiology_1tomany_2020.pdf
|authors=Hinson CM, Bardo AM, Shannon CE, Rivera S, Swaminathan J, Marcotte EM, Anslyn EV
|link=https://doi.org/10.1371/journal.pbio.3000627
|journal=Langmuir
|pubmed=32421706
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|comment=[https://www.biorxiv.org/content/10.1101/668335v1 bioRxiv preprint] (deposited June 13, 2019)
|volume=37(51)  
|page=14856–14865
|pdf=Langmuir_SurfacePrep_2021.pdf
|link=https://doi.org/10.1021/acs.langmuir.1c02644
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<li value="207"> {{Paper
</li>
|title=Functional partitioning of a liquid-like organelle during assembly of axonemal dyneins
<li value="223"> {{Paper
|authors=Lee C, Cox RM, Papoulas O, Horani A, Drew K, Devitt CC, Brody SL, Marcotte EM, Wallingford JB
|title=HumanNet v3: an improved database of human gene networks for disease research
|journal=eLife
|authors=Kim CY, Baek S, Cha J, Yang S, Kim E, Marcotte EM, Hart T, Lee I
|pub_year=2020
|journal=Nucleic Acids Res
|volume=9
|pub_year=2021
|pubmed=33263282
|volume=Nov 8:gkab1048
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|pdf=NAR_HumanNet3_2021.pdf
|pdf=eLife_DynAP_Partitioning_2020.pdf
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</li>
|title=A pan-plant protein complex map reveals deep conservation and novel assemblies
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|authors=McWhite CD, Papoulas O, Drew K, Cox RM, June V, Dong OX, Kwon T, Wan C, Salmi ML, Roux, SJ Jr., Browning KS, Chen ZJ, Ronald PC, Marcotte EM
|title=Photoredox-catalyzed decarboxylative C-terminal differentiation for bulk and single molecule proteomics
|journal=Cell
|authors=Zhang L, Floyd BM, Chilamari M, Mapes J, Swaminathan J, Bloom S, Marcotte EM, Anslyn EV
|pub_year=2020
|link=https://pubs.acs.org/doi/10.1021/acschembio.1c00631
|volume=181(2)
|journal=ACS Chem Biol
|pubmed=32191846
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|page=460-474.e14
|volume=16
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|link=https://doi.org/10.1016/j.cell.2020.02.049
|pdf=ACSChemBio_Cterm_2021.pdf
|pdf=Cell_PlantComplexes_2020.pdf
|comment=[https://doi.org/10.1101/2021.07.08.451692 bioRxiv preprint] (deposited July 9, 2021)
|pubmed=34734691
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}}
<li value="205"> {{Paper
</li>
|title=Structural Biology in the Multi-Omics Era
<li value="221"> {{Paper
|authors=McCafferty C, Verbeke EJ, Marcotte EM, Taylor DW
|title=Super.Complex: A supervised machine learning pipeline for molecular complex detection in protein-interaction networks
|journal=Journal of Chemical Information and Modeling
|authors=Palukuri MV, Marcotte EM
|pub_year=2020
|journal=PLoS One
|volume=60(5)
|pub_year=2021
|pubmed=32129623
|volume=16(12)
|page=2424-2429
|page=e0262056
|link=https://doi.org/10.1021/acs.jcim.9b01164
|pdf=PLoSOne_SuperComplex_2021.pdf
|comment=[[File:JCIMShotgunEMCover2020.jpg||100px|right]]
|comment=[https://doi.org/10.1101/2021.06.22.449395 bioRxiv preprint] (deposited October 11, 2021)
|pdf=JChemInfModel_Structural-Omics_2020.pdf
|link=https://doi.org/10.1371/journal.pone.0262056
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<li value="204"> {{Paper
</li>
|title=Abundances of transcripts, proteins, and metabolites in the cell cycle of budding yeast reveals coordinate control of lipid metabolism
<li value="220"> {{Paper
|authors=Blank HM, Papoulas O, Maitra N, Garge RK, Kennedy BK, Schilling B, Marcotte EM, Polymenis M
|title=Discovery of new vascular disrupting agents based on evolutionarily conserved drug action, pesticide resistance mutations, and humanized yeast
|journal=Molecular Biology of the Cell
|authors=Garge RK, Cha HJ, Lee, C, Gollihar JD, Kachroo AH, Wallingford JB, Marcotte EM
|pub_year=2020
|journal=Genetics
|volume=31
|pub_year=2021
|pubmed=32129706
|volume=219(1)
|page=1061-1084
|pdf=Genetics_VDAs_2021.pdf
|link=https://www.molbiolcell.org/doi/abs/10.1091/mbc.E19-12-0708
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|page=iyab101
|pdf=MolBiolCell_YeastCellCycle_2020.pdf
|comment=[https://doi.org/10.1101/2020.09.15.298828 bioRxiv preprint] (deposited Sept 15, 2020 under the title '''Antifungal benzimidazoles disrupt vasculature by targeting one of nine β-tubulins''') [https://genestogenomes.org/how-an-anti-fungal-medication-can-stop-new-blood-vessel-formation/ Commentary] [[File:GeneticsVDACover2021.jpg|100px|right]]
|pubmed=34849907
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<li value="203"> {{Paper
</li>
|title=A systematic, label-free method for identifying RNA-associated proteins in vivo provides insights into vertebrate ciliary beating
<li value="219"> {{Paper
|authors=Drew K, Lee C, Cox RM, Dang V, Devitt CC, Papoulas O, Huizar RL, Marcotte EM, Wallingford JB
|title=Functional expression of opioid receptors and other human GPCRs in yeast engineered to produce human sterols
|journal=Developmental Biology
|authors=Bean BDM, Mulvihill C, Garge RK, Boutz DR, Rousseau O, Floyd BM, Cheney W, Gardner EC, Ellington AD, Marcotte EM, Gollihar JD, Whiteway M, Martin VJJ
|pub_year=2020
|journal=Nature Communications
|volume=467(1-2)
|pub_year=2022
|comment=[https://doi.org/10.1101/2020.02.26.966754 bioRxiv preprint] (deposited Feb 27, 2020)
|volume=13(1)
|link=https://www.sciencedirect.com/science/article/abs/pii/S0012160620302293
|page=2882
|pdf=DevelopmentalBiology_DIFFRAC-DynAPs_2020.pdf
|pdf=NatureCommunications_OpioidReceptorStrains_2022.pdf
|pubmed=32898505
|comment=[https://doi.org/10.1101/2021.05.12.443385 bioRxiv preprint] (deposited May 14, 2021)
|page=108-117
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<li value="202"> {{Paper
<li value="218"> {{Paper
|title=Mapping functional protein neighborhoods in the mouse brain
|title=The emerging landscape of single-molecule protein sequencing technologies
|authors=Liebeskind BJ, Young RL, Halling DB, Aldrich RW, Marcotte EM
|authors=Alfaro J, Bohländer P, Dai M, Filius M, Howard CJ, van  Kooten XF, Ohayon S, Pomorski A, Schmid S, Aksimentiev A, Anslyn EV, Bedran G, Chan C, Chinappi M, Coyaud E, Dekker C, Dittmar G, Drachman N, Eelkema R, Goodlett D, Hentz S, Kalathiya U, Kelleher NL, Kelly RT, Kelman Z, Kim SH, Kuster B, Rodriguez-Larrea D, Lindsey S, Maglia G, Marcotte EM, Marino JP, Masselon C, Mayer M, Samaras P, Sarthak K, Sepiashvili L, Stein D, Wanunu M, Wilhelm M, Yin P, Meller A, Joo C
|journal=Nature Methods
|pub_year=2021
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|title=Synthetic repertoires derived from convalescent COVID-19 patients enable discovery of SARS-CoV-2 neutralizing antibodies and a novel quaternary binding modality
|authors=Goike J, Hsieh C-L, Horton A, Gardner AC, Bartzoka F, Wang N,  Javanmardi K, Herbert A, Abbassi S, Renberg R, Johanson MJ, Cardona JA, Segall-Shapiro T, Zhou L, Nissly RH, Gontu A, Byrom M, Maranhao AC, Battenhouse AM, Gejji V, Soto-Sierra L, Foster ER, Woodard SL, Nikolov ZL, Lavinder J, Voss WN, Annapareddy A, Ippolito GC, Ellington AD, Marcotte EM, Finkelstein IJ, Hughes RA, Musser JM, Kuchipudi SJ, Kapur V, Georgiou G, Dye JM, Boutz DR, McLellan JS, Gollihar JD
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|pub_year=2021
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|volume=Posted April 9
|link=https://doi.org/10.1101/2020.01.26.920447
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|link=https://doi.org/10.1101/2021.04.07.438849
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<li value="216"> {{Paper
|title= Solid-phase peptide capture and release for bulk and single-molecule proteomics
|title=Co-fractionation/mass spectrometry to identify protein complexes
|authors=Howard CJ, Floyd BM, Bardo AM, Swaminathan J, Marcotte EM, Anslyn EV
|authors=McWhite CD, Papoulas O, Drew K, Dang V, Leggere JC, Sae-Lee W, Marcotte EM
|journal=ACS Chemical Biology
|journal=STAR Protocols
|pub_year=2020
|pub_year=2021
|volume=15(6)
|volume=2(1)
|link=https://doi.org/10.1021/acschembio.0c00040
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|pdf=STARProtocols_cfms_2021.pdf
|pdf=ACSChemBio_Marbles_2020.pdf
|link=https://www.sciencedirect.com/science/article/pii/S2666166721000770
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|title=Separating distinct structures of multiple macromolecular assemblies from cryo-EM projections
|title=Spatiotemporal transcriptional dynamics of the cycling mouse oviduct
|authors=Verbeke E, Zhou Y, Horton AP, Mallam AL, Taylor DW, Marcotte EM
|authors=Roberson E, Battenhouse A, Garge RK, Tran NK, Marcotte EM, Wallingford JB
|journal=Journal of Structural Biology
|journal=Developmental Biology
|pub_year=2020
|pub_year=2021
|volume=209(1)
|volume=476 (2021)
|link=https://doi.org/10.1016/j.jsb.2019.107416
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|page=107416
|link=https://doi.org/10.1016/j.ydbio.2021.03.018
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|link=https://doi.org/10.1016/j.jsb.2019.107416
|pdf=DevelopmentalBiology_mouseoviduct_2021.pdf
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<li value="199"> {{Paper
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|title=Synthesis of Carboxy ATTO 647N Using Redox Cycling for Xanthone Access
<li value="214"> {{Paper
|authors=Bachman JL, Pavlich CI, Boley AJ, Marcotte EM, Anslyn EV
|title=Improving integrative 3D modeling into low- to medium- resolution EM structures with evolutionary couplings
|journal=Org Lett
|authors=McCafferty CL, Taylor DW, Marcotte EM
|pub_year=2020
|journal=Protein Science
|volume=22(2)
|pub_year=2021
|link=https://doi.org/10.1021/acs.orglett.9b03981
|volume=30
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|page=1006–1021
|page=381-385
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|link=https://pubs.acs.org/doi/10.1021/acs.orglett.9b03981
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</li>
</li>
</ol>
</ol>


== 2019 ==
== 2020 ==
<ol>
<ol>  
<li value="198"> {{Paper
<li value="213"> {{Paper
|title=Simplified geometric representations of protein structures identify complementary interaction interfaces
|title=Systematic Identification of Protein Phosphorylation-Mediated Interactions
|authors=McCafferty CL, Marcotte EM, Taylor DW
|authors=Floyd BM, Drew K, Marcotte EM
|journal=Proteins: Structure, Function, and Bioinformatics
|journal=J Proteome Research
|pub_year=2021
|pub_year=2021
|volume=89(3)
|volume=20(2)
|page=348-360
|page=1359-1370
|pubmed=33140424
|pdf=JProteomeResearch_PhosphoDIFFRAC_2021.pdf
|link=https://doi.org/10.1002/prot.26020
|link=https://doi.org/10.1021/acs.jproteome.0c00750
|comment=[https://doi.org/10.1101/2019.12.18.880575 bioRxiv preprint] (deposited Dec 23, 2019)
|comment=[https://doi.org/10.1101/2020.09.18.304121 bioRxiv preprint] (deposited Sept 19, 2020)
|journal=Proteins: Structure, Function, and Bioinformatics
|pubmed=33476154
|pdf=Proteins_SimplifiedRepresentation_2020.pdf
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}}
<li value="197"> {{Paper
</li>
|title=Systematic bromodomain protein screens identify homologous recombination and R-loop suppression pathways involved in genome integrity
<li value="212"> {{Paper
|authors=Kim JJ, Lee SY, Gong F, Battenhouse AM, Boutz DR, Bashyal A, Refvik ST, Chiang CM, Xhemalce B, Paull TT, Brodbelt JS, Marcotte EM, Miller KM
|title=hu.MAP 2.0: Integration of over 15,000 proteomic experiments builds a global compendium of human multiprotein assemblies
|journal=Genes and Development
|authors=Drew K, Wallingford JB, Marcotte EM
|pub_year=2019
|journal=Molecular Systems Biology
|volume=33(23-24)
|pub_year=2021
|pubmed=31753913
|volume=17
|page=1751-1774
|pdf=MolecularSystemsBiology_HuMap2_2021.pdf
|pdf=GenesDev_Bromodomains_2019.pdf
|link=https://doi.org/10.15252/msb.202010016
|link=https://doi.org/10.1101/gad.331231.119
|page=e10016
|comment=[https://doi.org/10.1101/2020.09.15.298216 bioRxiv preprint] (deposited Sept 16, 2020)
|pubmed=33973408
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}}
<li value="196"> {{Paper
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|title=Systematic discovery of endogenous human ribonucleoprotein complexes
<li value="211"> {{Paper
|authors=Mallam AL, Sae-Lee W, Schaub JM, Tu F, Battenhouse A, Jang YJ, Kim J, Finkelstein IJ, Marcotte EM, Drew K
|title=Twinfilin1 controls lamellipodial protrusive activity and actin turnover during vertebrate gastrulation
|journal=Cell Reports
|authors=Devitt C, Lee C, Cox R, Papoulas O, Alvarado J, Marcotte EM, Wallingford JB
|pub_year=2019
|journal=J Cell Science
|volume=29(5)
|pub_year=2021
|page=P1351-1368.e5
|volume=134(14)
|pubmed=31665645
|link=https://doi.org/10.1242/jcs.254011
|pdf=CellReports_DIFFRAC_2019.pdf
|pdf=JCellSci_Twinfilin_2021.pdf
|link=https://doi.org/10.1016/j.celrep.2019.09.060
|page=jcs254011
|comment=[https://www.biorxiv.org/content/early/2018/11/27/480061 bioRxiv preprint] (deposited Nov 27, 2018)
|comment=[https://doi.org/10.1101/2020.09.03.281659 bioRxiv preprint] (deposited September 3, 2020) [https://journals.biologists.com/jcs/article/134/14/e134_e1401/270993/Linking-actin-regulatory-machinery-to-vertebrate Research Highlight]
|pubmed=34060614
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}}
<li value="195"> {{Paper
</li>
|title=Ancestral Reconstruction of Protein Interaction Networks
<li value="210"> {{Paper
|authors=Liebeskind B, Aldrich RW, Marcotte EM
|title=Next-Generation TLC: A Quantitative Platform for Parallel Spotting and Imaging
|journal=PLoS Computational Biology
|authors=Boulgakov AA, Moor SR, Jo HH, Metola P, Joyce LA, Marcotte EM, Welch CJ, Anslyn EV
|pub_year=2019
|journal=J Org Chem
|volume=15(10)
|pub_year=2020
|page=e1007396
|volume=85(15)  
|pubmed=31658251
|page=9447–9453
|pdf=PLoSComputationalBiology_AncestralPPIs_2019.pdf
|pdf=JOrgChem_NextGenTLC_2020.pdf
|link= https://doi.org/10.1371/journal.pcbi.1007396
|link=https://doi.org/10.1021/acs.joc.0c00349
|comment=[https://doi.org/10.1101/408773 bioRxiv preprint] (deposited September 9, 2018)
|comment=[[File:JOC-TLCCover2020.jpg||100px|right]]
|pubmed=32559382
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<li value="194"> {{Paper
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|title=Advances and Applications in the Quest for Orthologs.
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|authors=Glover N, Dessimoz C, Ebersberger I, Forslund SK, Gabaldón T, Huerta-Cepas J, Martin MJ, Muffato M, Patricio M, Pereira C, Sousa da Silva A, Wang Y, Sonnhammer E, Thomas PD; Quest for Orthologs Consortium
|title=Systematic humanization of the yeast cytoskeleton discerns functionally replaceable from divergent human genes
|journal=Mol Biol Evol
|authors=Garge RK, Laurent JM, Kachroo AH, Marcotte EM
|pub_year=2019
|journal=Genetics
|volume=36(10)
|pub_year=2020
|page=2157-2164
|volume=215(4)
|pdf=MolBiolEvol_QfO_2019.pdf
|pubmed=32522745
|link=https://doi.org/10.1093/molbev/msz150
|page=1153-1169
|pubmed=31241141
|pdf=Genetics_HumanizingCytoskeleton_2020.pdf
|comment=[https://doi.org/10.1101/2019.12.16.878751 bioRxiv preprint] (deposited December 17, 2019) [[File:GeneticsHumanizedYeastCover2020.jpg||100px|right]]
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}}
<li value="193"> {{Paper
</li>
|title=Bringing Microscopy-By-Sequencing into View
<li value="208"> {{Paper
|authors=Boulgakov AA, Ellington AD, Marcotte EM
|title=Humanization of yeast genes with multiple human orthologs reveals principles of functional divergence between paralogs
|journal=Trends in Biotechnology
|authors=Laurent J, Garge RK, Teufel AI, Wilke CO, Kachroo AH, Marcotte EM
|pub_year=available online 2019, published 2020
|journal=PLoS Biology
|volume=38(2)
|pub_year=2020
|page=154-162
|volume=18(5)
|pubmed=31416630
|page=e3000627
|pdf=TIBTech_DNAmicroscopy_2020.pdf
|pdf=PLoSBiology_1tomany_2020.pdf
|link=https://doi.org/10.1016/j.tibtech.2019.06.001
|link=https://doi.org/10.1371/journal.pbio.3000627
|comment=[[File:TIBTechCover2020.jpg||100px|right]]
|pubmed=32421706
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}}
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</li>
</ol>
<li value="207"> {{Paper
 
|title=Functional partitioning of a liquid-like organelle during assembly of axonemal dyneins
== 2018 ==
|authors=Lee C, Cox RM, Papoulas O, Horani A, Drew K, Devitt CC, Brody SL, Marcotte EM, Wallingford JB
<ol>
|journal=eLife
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|title=Paternal chromosome loss and metabolic crisis contribute to hybrid inviability in ''Xenopus''
|volume=9
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|pubmed=33263282
|journal=Nature
|page=e58662
|volume=553
|link=https://doi.org/10.7554/eLife.58662
|page=337–341
|pdf=eLife_DynAP_Partitioning_2020.pdf
|pubmed=29320479
|comment=[https://doi.org/10.1101/2020.04.21.052837 bioRxiv preprint] (deposited April 21, 2020)
|pub_year=2018
|pdf=Nature_XenopusHybridInviability_2017.pdf
|link=http://dx.doi.org/10.1038/nature25188
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|title=A liquid-like organelle at the root of motile ciliopathy
<li value="206"> {{Paper
|authors=Huizar RL, Lee C, Boulgakov AA, Horani A, Tu F, Marcotte EM, Brody SL, Wallingford JB
|title=A pan-plant protein complex map reveals deep conservation and novel assemblies
|journal=eLife
|authors=McWhite CD, Papoulas O, Drew K, Cox RM, June V, Dong OX, Kwon T, Wan C, Salmi ML, Roux, SJ Jr., Browning KS, Chen ZJ, Ronald PC, Marcotte EM
|pub_year=2018
|journal=Cell
|comment=[https://doi.org/10.1101/213793 bioRxiv preprint (deposited Nov 3, 2017)]
|pub_year=2020
|volume=7
|volume=181(2)
|pubmed=30561330
|pubmed=32191846
|page=e38497
|page=460-474.e14
|pdf=eLife_DynAPs_2018.pdf
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|link=https://doi.org/10.1016/j.cell.2020.02.049
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|title=From Space to Sequence and Back Again: Iterative DNA Proximity Ligation and its Applications to DNA-Based Imaging
<li value="205"> {{Paper
|authors=Boulgakov AA, Xiong E, Bhadra S, Ellington AD, Marcotte EM
|title=Structural Biology in the Multi-Omics Era
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|authors=McCafferty C, Verbeke EJ, Marcotte EM, Taylor DW
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|journal=Journal of Chemical Information and Modeling
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|volume=60(5)
|link=https://doi.org/10.1101/470211
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|page=2424-2429
|link=https://doi.org/10.1021/acs.jcim.9b01164
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<li value="189"> {{Paper
</li>
|title=HumanNet v2: human gene networks for disease research
<li value="204"> {{Paper
|authors=Hwang S, Kim CY, Yang S, Kim E, Hart T, Marcotte EM, Lee I
|title=Abundances of transcripts, proteins, and metabolites in the cell cycle of budding yeast reveals coordinate control of lipid metabolism
|journal=Nucleic Acids Res
|authors=Blank HM, Papoulas O, Maitra N, Garge RK, Kennedy BK, Schilling B, Marcotte EM, Polymenis M
|pub_year=2018,2019
|journal=Molecular Biology of the Cell
|volume=47 (D1)
|pub_year=2020
|page=D573–D580
|volume=31
|pdf=NAR_HumanNet2_2018.pdf
|pubmed=32129706
|link=https://doi.org/10.1093/nar/gky1126
|page=1061-1084
|pubmed=30418591
|link=https://www.molbiolcell.org/doi/abs/10.1091/mbc.E19-12-0708
|comment=[https://doi.org/10.1101/2019.12.17.880252 bioRxiv preprint] (deposited Dec 18, 2019)
|pdf=MolBiolCell_YeastCellCycle_2020.pdf
}}
}}
<li value="188"> {{Paper
</li>
|title=Highly parallel single-molecule identification of proteins in zeptomole-scale mixtures
<li value="203"> {{Paper
|authors=Swaminathan J, Boulgakov AA, Hernandez ET, Bardo AM, Bachman JL, Marotta J, Johnson AM, Anslyn EV, Marcotte EM
|title=A systematic, label-free method for identifying RNA-associated proteins in vivo provides insights into vertebrate ciliary beating
|journal=Nature Biotechnology
|authors=Drew K, Lee C, Cox RM, Dang V, Devitt CC, Papoulas O, Huizar RL, Marcotte EM, Wallingford JB
|pub_year=2018
|journal=Developmental Biology
|volume=36
|pub_year=2020
|page=1076–1082
|volume=467(1-2)
|pubmed=30346938
|comment=[https://doi.org/10.1101/2020.02.26.966754 bioRxiv preprint] (deposited Feb 27, 2020)
|pdf=NatureBiotechnology_Fluorosequencing_2018.pdf
|link=https://www.sciencedirect.com/science/article/abs/pii/S0012160620302293
|link=https://doi.org/10.1038/nbt.4278
|pdf=DevelopmentalBiology_DIFFRAC-DynAPs_2020.pdf
|comment=[https://rdcu.be/9Pjj Free access authors' view-only version at NBT] [http://www.marcottelab.org/paper-pdfs/NatureBiotechnology_Fluorosequencing_2018_Supplement.pdf Supplement] [http://www.marcottelab.org/paper-pdfs/NatureBiotechnology_Fluorosequencing_2018_SupplementaryTables.pdf Supplementary Tables] [https://github.com/marcottelab/FluorosequencingImageAnalysis/ github with code] [http://doi.org/10.5281/zenodo.782860 Data repository (Zenodo)] [http://www.marcottelab.org/paper-pdfs/NatureBiotechnology_Fluorosequencing_2018_NewsAndViews-CollinsAebsersold.pdf News & Views] Commentary in [https://phys.org/news/2018-10-protein-sequencing-method-biological.html Phys.org] 
|pubmed=32898505
|page=108-117
}}
}}
<li value="187"> {{Paper
</li>
|title=The many nuanced evolutionary consequences of duplicated genes
<li value="202"> {{Paper
|authors=Teufel AI, Johnson MM, Laurent JM, Kachroo AH, Marcotte EM, Wilke CO
|title=Mapping functional protein neighborhoods in the mouse brain
|journal=Mol Bio Evol
|authors=Liebeskind BJ, Young RL, Halling DB, Aldrich RW, Marcotte EM
|pub_year=2018
|journal=bioRxiv
|volume=36(2)
|pub_year=2020
|page=304-314
|volume=Posted January 27
|pdf=MolBiolEvol_Teufel_2018.pdf
|link=https://doi.org/10.1101/2020.01.26.920447
|link=https://academic.oup.com/mbe/article-lookup/doi/10.1093/molbev/msy210
|pubmed=
|comment = [https://doi.org/10.1101/366971 bioRxiv preprint] (deposited July 10, 2018)
|page=
|pubmed=30428072
}}
}}
<li value="186"> {{Paper
</li>
|title=Photography Coupled with Self-Propagating Chemical Cascades. The Differentiation and Quantitation of G and V Nerve Agent Mimics via Chromaticity
<li value="201"> {{Paper
|authors=Sun X, Boulgakov AA, Smith L, Metola P, Marcotte EM, Anslyn EV
|title= Solid-phase peptide capture and release for bulk and single-molecule proteomics
|journal=ACS Central Science
|authors=Howard CJ, Floyd BM, Bardo AM, Swaminathan J, Marcotte EM, Anslyn EV
|volume=4(7)
|journal=ACS Chemical Biology
|page=854-861
|pub_year=2020
|pubmed=30062113
|volume=15(6)
|pub_year=2018
|link=https://doi.org/10.1021/acschembio.0c00040
|pdf=ACSCentralScience_LegoNerveGas_2018.pdf
|comment=[http://www.marcottelab.org/paper-pdfs/ACSChemBio_Marbles_2020_supplement.pdf Supplement] [https://doi.org/10.1101/2020.01.13.904540 bioRxiv preprint] (deposited January 14, 2020)
|link=https://pubs.acs.org/doi/10.1021/acscentsci.8b00193
|pdf=ACSChemBio_Marbles_2020.pdf
|pubmed=32363853
|page=1401-1407
}}
}}
<li value="185"> {{Paper
</li>
|title=Classification of single particles from human cell extract reveals distinct structures
<li value="200"> {{Paper
|authors=Verbeke EJ, Mallam AL, Drew K, Marcotte EM, Taylor DW
|title=Separating distinct structures of multiple macromolecular assemblies from cryo-EM projections
|journal=Cell Reports
|authors=Verbeke E, Zhou Y, Horton AP, Mallam AL, Taylor DW, Marcotte EM
|volume=(24)1
|journal=Journal of Structural Biology
|page=259–268.e3
|pub_year=2020
|link=https://doi.org/10.1016/j.celrep.2018.06.022
|volume=209(1)
|pubmed=29972786
|link=https://doi.org/10.1016/j.jsb.2019.107416
|pdf=CellReports_ShotgunEM_2018.pdf
|pubmed=31726096
|pub_year=2018
|page=107416
|comment = [https://www.biorxiv.org/content/early/2018/01/14/247254 bioRxiv preprint] (deposited January 14 , 2018)
|pdf=JStructBiol_SLICEM_2019.pdf
|link=https://doi.org/10.1016/j.jsb.2019.107416
|comment=[https://github.com/marcottelab/SLICEM SLICEM code on Github] [https://www.biorxiv.org/content/10.1101/611566v1 bioRxiv preprint] (deposited Apr 20, 2019)
}}
}}
<li value="184"> {{Paper
</li>
|title=Single-step precision genome editing in yeast using CRISPR-Cas9   
<li value="199"> {{Paper
|authors= Akhmetov A, Laurent JM, Gollihar J, Gardner EC, Garge RK, Ellington AD, Kachroo AH, Marcotte EM  
|title=Synthesis of Carboxy ATTO 647N Using Redox Cycling for Xanthone Access
|journal=Bio-protocol
|authors=Bachman JL, Pavlich CI, Boley AJ, Marcotte EM, Anslyn EV
|volume=8(6)
|journal=Org Lett
|page=e2765
|pub_year=2020
|pubmed=29770349
|volume=22(2)
|pub_year=2018
|link=https://doi.org/10.1021/acs.orglett.9b03981
|pdf=Bio-protocol_YeastCRISPR_2018.pdf
|pubmed=31825225
|link=http://dx.doi.org/10.21769/BioProtoc.2765
|page=381-385
|pdf=OrganicLetters_Atto647N_2020.pdf
|link=https://pubs.acs.org/doi/10.1021/acs.orglett.9b03981
}}
}}
</li>
</li>
<li value="183"> {{Paper
</ol>
|title=Protein localization screening in vivo reveals novel regulators of multiciliated cell development and function
|authors=Tu F, Sedzinski J, Ma Y, Marcotte EM, Wallingford JB
|journal=J Cell Sci
|volume=131 (3)
|page=jcs206565
|pubmed=29180514
|pub_year=2018
|pdf=JCellSci_CiliaScreen_2018.pdf
|link=http://jcs.biologists.org/content/131/3/jcs206565
|comment=[[File:JCSCiliaCover2018.jpg||100px|right]]
}}
</li>
</ol>


== 2017 ==
== 2019 ==
<ol>
<ol>
<li value="182"> {{Paper
<li value="198"> {{Paper
|title=Solution-phase and solid-phase sequential, selective modification of side chains in KDYWEC and KDYWE as models for usage in single-molecule protein sequencing
|title=Simplified geometric representations of protein structures identify complementary interaction interfaces
|authors=Hernandez ET, Swaminathan J, Marcotte EM , Anslyn EV
|authors=McCafferty CL, Marcotte EM, Taylor DW
|journal=New Journal of Chemistry
|journal=Proteins: Structure, Function, and Bioinformatics
|pubmed=
|pub_year=2021
|volume=41
|volume=89(3)
|pubmed=28983186
|page=348-360
|page=462-469
|pubmed=33140424
|link=http://dx.doi.org/10.1039/C6NJ02932A
|link=https://doi.org/10.1002/prot.26020
|pub_year=2017
|comment=[https://doi.org/10.1101/2019.12.18.880575 bioRxiv preprint] (deposited Dec 23, 2019)
|pdf=NewJChem_PeptideLabeling_2017.pdf
|journal=Proteins: Structure, Function, and Bioinformatics
|comment=[[File:NJCPeptideLabelingCover2017.jpg||100px|right]]
|pdf=Proteins_SimplifiedRepresentation_2020.pdf
}}
</li>
<li value="197"> {{Paper
|title=Systematic bromodomain protein screens identify homologous recombination and R-loop suppression pathways involved in genome integrity
|authors=Kim JJ, Lee SY, Gong F, Battenhouse AM, Boutz DR, Bashyal A, Refvik ST, Chiang CM, Xhemalce B, Paull TT, Brodbelt JS, Marcotte EM, Miller KM
|journal=Genes and Development
|pub_year=2019
|volume=33(23-24)
|pubmed=31753913
|page=1751-1774
|pdf=GenesDev_Bromodomains_2019.pdf
|link=https://doi.org/10.1101/gad.331231.119
}}
</li>
<li value="196"> {{Paper
|title=Systematic discovery of endogenous human ribonucleoprotein complexes
|authors=Mallam AL, Sae-Lee W, Schaub JM, Tu F, Battenhouse A, Jang YJ, Kim J, Finkelstein IJ, Marcotte EM, Drew K
|journal=Cell Reports
|pub_year=2019
|volume=29(5)
|page=P1351-1368.e5
|pubmed=31665645
|pdf=CellReports_DIFFRAC_2019.pdf
|link=https://doi.org/10.1016/j.celrep.2019.09.060
|comment=[https://www.biorxiv.org/content/early/2018/11/27/480061 bioRxiv preprint] (deposited Nov 27, 2018)
}}
}}
<li value="181"> {{Paper
</li>
|title=Identifying direct contacts between protein complex subunits from their conditional dependence in proteomics datasets
<li value="195"> {{Paper
|authors=Drew K, Müller CL, Bonneau R, Marcotte EM
|title=Ancestral Reconstruction of Protein Interaction Networks
|authors=Liebeskind B, Aldrich RW, Marcotte EM
|journal=PLoS Computational Biology
|journal=PLoS Computational Biology
|volume=13(10)
|pub_year=2019
|page=e1005625
|volume=15(10)
|pubmed=29023445
|page=e1007396
|pub_year=2017
|pubmed=31658251
|pdf=PLoSComputationalBiology-ConditionalDependencePPIs-2017.pdf
|pdf=PLoSComputationalBiology_AncestralPPIs_2019.pdf
|link=https://doi.org/10.1371/journal.pcbi.1005625
|link= https://doi.org/10.1371/journal.pcbi.1007396
|comment=[https://doi.org/10.1101/408773 bioRxiv preprint] (deposited September 9, 2018)
}}
}}
<li value="180"> {{Paper
</li>
|title=Metabolic crosstalk regulates ''Porphyromonas gingivalis'' colonization and virulence during oral polymicrobial infection
<li value="194"> {{Paper
|authors=Kuboniwa M, Houser JR, Hendrickson EL, Wang Q, Alghamdi SA, Sakanaka A, Miller DP, Hutcherson JA, Wang T, Beck DAC, Whiteley M, Amano A, Wang H, Marcotte EM, Hackett M, Lamont RJ
|title=Advances and Applications in the Quest for Orthologs.
|journal=Nature Microbiology
|authors=Glover N, Dessimoz C, Ebersberger I, Forslund SK, Gabaldón T, Huerta-Cepas J, Martin MJ, Muffato M, Patricio M, Pereira C, Sousa da Silva A, Wang Y, Sonnhammer E, Thomas PD; Quest for Orthologs Consortium
|volume=2
|journal=Mol Biol Evol
|page=1493–1499
|pub_year=2019
|pubmed=28924191
|volume=36(10)
|pub_year=2017
|page=2157-2164
|pdf=NatureMicrobiology_PolymicrobialInfection_2017.pdf
|pdf=MolBiolEvol_QfO_2019.pdf
|link=https://doi.org/10.1038/s41564-017-0021-6
|link=https://doi.org/10.1093/molbev/msz150
|pubmed=31241141
}}
}}
<li value="179"> {{Paper
</li>
|title=Systematic bacterialization of yeast genes identifies a near-universally swappable pathway
<li value="193"> {{Paper
|authors=Kachroo AH, Laurent JM, Akhmetov A, Szilagyi-Jones M, McWhite CD, Zhao A, Marcotte EM
|title=Bringing Microscopy-By-Sequencing into View
|journal=eLife
|authors=Boulgakov AA, Ellington AD, Marcotte EM
|volume=6
|journal=Trends in Biotechnology
|page=e25093
|pub_year=available online 2019, published 2020
|pubmed=28661399
|volume=38(2)
|pub_year=2017
|page=154-162
|pdf=eLife_BacterializedYeast_2017.pdf
|pubmed=31416630
|link=https://doi.org/10.7554/eLife.25093
|pdf=TIBTech_DNAmicroscopy_2020.pdf
|link=https://doi.org/10.1016/j.tibtech.2019.06.001
|comment=[[File:TIBTechCover2020.jpg||100px|right]]
}}
}}
<li value="178"> {{Paper
</li>
|title=A highly parallel strategy for storage of digital information in living cells
</ol>
|authors=Akhmetov A, Ellington A, Marcotte E
 
|journal=BMC Biotechnology
== 2018 ==
|volume=18
<ol>
|page=64
<li value="192"> {{Paper
|pubmed=30333005
|title=Paternal chromosome loss and metabolic crisis contribute to hybrid inviability in ''Xenopus''
|pdf=bioRxiv_DigitalDNAStorage_2016.pdf
|authors=Gibeaux R, Acker R, Kitaoka M, Georgiou G, van Kruijsbergen I, Ford B, Marcotte EM, Nomura DK, Kwon T, Veenstra GJC, Heald R
|journal=Nature
|volume=553
|page=337–341
|pubmed=29320479
|pub_year=2018
|pub_year=2018
|comment = [https://doi.org/10.1101/096792 bioRxiv preprint (deposited December 26, 2016)] [https://rdcu.be/9u6Y Open access pdf version of the article]
|pdf=Nature_XenopusHybridInviability_2017.pdf
|link=https://doi.org/10.1186/s12896-018-0476-4
|link=http://dx.doi.org/10.1038/nature25188
}}
}}
<li value="177"> {{Paper
</li>
|title=Systems-wide studies uncover Commander, a multiprotein complex essential to human development
<li value="191"> {{Paper
|authors=Mallam A, Marcotte EM
|title=A liquid-like organelle at the root of motile ciliopathy
|journal=Cell Systems
|authors=Huizar RL, Lee C, Boulgakov AA, Horani A, Tu F, Marcotte EM, Brody SL, Wallingford JB
|volume=4
|journal=eLife
|page=483-494
|pub_year=2018
|pubmed=28544880
|comment=[https://doi.org/10.1101/213793 bioRxiv preprint (deposited Nov 3, 2017)]
|link=http://www.cell.com/cell-systems/abstract/S2405-4712(17)30138-2
|volume=7
|pdf=CellSystems_Commander_2017.pdf
|pubmed=30561330
|pub_year=2017
|page=e38497
|pdf=eLife_DynAPs_2018.pdf
|link=https://doi.org/10.7554/eLife.38497
}}
}}
<li value="176"> {{Paper
</li>
|title=Integration of over 9,000 mass spectrometry experiments builds a global map of human protein complexes
<li value="190"> {{Paper
|authors=Drew, K., Lee, C., Huizar, R. L., Tu, F., Borgeson, B., McWhite, C. D., Ma, Y., Wallingford, J. B., Marcotte, E. M.
|title=From Space to Sequence and Back Again: Iterative DNA Proximity Ligation and its Applications to DNA-Based Imaging
|journal=Molecular Systems Biology
|authors=Boulgakov AA, Xiong E, Bhadra S, Ellington AD, Marcotte EM
|page=932
|journal=bioRxiv
|volume=13
|pub_year=2018
|pubmed=28596423
|volume=posted November 14
|link=http://msb.embopress.org/content/13/6/932
|page=
|pdf=MolecularSystemsBiology_2017_HuMap.pdf
|link=https://doi.org/10.1101/470211
|comment = [https://doi.org/10.1101/092361 bioRxiv preprint (deposited December 7, 2016)] [[File:MSBHuMAPCover2018.jpg||100px|right]]
|pub_year=2017
}}
}}
<li value="175"> {{Paper
</li>
|title=GWAB: a web server for the network-based boosting of human genome-wide association data
<li value="189"> {{Paper
|authors=Shim JE, Bang C, Yang S, Lee T, Hwang S, Kim CY, Singh-Blom UM, Marcotte EM, Lee I
|title=HumanNet v2: human gene networks for disease research
|journal=Nucleic Acids Research
|authors=Hwang S, Kim CY, Yang S, Kim E, Hart T, Marcotte EM, Lee I
|pubmed=28449091
|journal=Nucleic Acids Res
|volume=89(6)
|pub_year=2018,2019
|page=3747–3753
|volume=47 (D1)
|link=http://dx.doi.org/10.1093/nar/gkx284
|page=D573–D580
|pub_year=2017
|pdf=NAR_HumanNet2_2018.pdf
|pdf=NAR_GWAB_2017.pdf
|link=https://doi.org/10.1093/nar/gky1126
|pubmed=30418591
}}
}}
<li value="174"> {{Paper
</li>
|title=The ''E. coli'' molecular phenotype under different growth conditions
<li value="188"> {{Paper
|authors=Caglar MU, Houser JR, Barnhart CS, Boutz DR, Carroll SM, Dasgupta A, Lenoir WF, Smith BL, Sridhara V, Sydykova DK, Vander Wood D, Marx CJ, Marcotte EM, Barrick JE, Wilke CO
|title=Highly parallel single-molecule identification of proteins in zeptomole-scale mixtures
|journal=Scientific Reports
|authors=Swaminathan J, Boulgakov AA, Hernandez ET, Bardo AM, Bachman JL, Marotta J, Johnson AM, Anslyn EV, Marcotte EM
|pubmed=28417974
|journal=Nature Biotechnology
|volume=7
|pub_year=2018
|page=45303
|volume=36
|link=http://dx.doi.org/10.1038/srep45303
|page=1076–1082
|pub_year=2017
|pubmed=30346938
|pdf=ScientificReports_EcoliMolecularPhenotype_2017.pdf
|pdf=NatureBiotechnology_Fluorosequencing_2018.pdf
|link=https://doi.org/10.1038/nbt.4278
|comment=[https://rdcu.be/9Pjj Free access authors' view-only version at NBT] [http://www.marcottelab.org/paper-pdfs/NatureBiotechnology_Fluorosequencing_2018_Supplement.pdf Supplement] [http://www.marcottelab.org/paper-pdfs/NatureBiotechnology_Fluorosequencing_2018_SupplementaryTables.pdf Supplementary Tables] [https://github.com/marcottelab/FluorosequencingImageAnalysis/ github with code] [http://doi.org/10.5281/zenodo.782860 Data repository (Zenodo)] [http://www.marcottelab.org/paper-pdfs/NatureBiotechnology_Fluorosequencing_2018_NewsAndViews-CollinsAebsersold.pdf News & Views] Commentary in [https://phys.org/news/2018-10-protein-sequencing-method-biological.html Phys.org] 
}}
}}
<li value="173"> {{Paper
</li>
|title=Large-scale analysis of post-translational modifications in ''E. coli'' under glucose-limiting conditions
<li value="187"> {{Paper
|authors=Brown CW, Sridhara V, Boutz DR, Person MD, Marcotte EM, Barrick JE, Wilke CO
|title=The many nuanced evolutionary consequences of duplicated genes
|journal=BMC Genomics
|authors=Teufel AI, Johnson MM, Laurent JM, Kachroo AH, Marcotte EM, Wilke CO
|pubmed=28412930
|journal=Mol Bio Evol
|volume=18(1)
|pub_year=2018
|page=301
|volume=36(2)
|link=http://dx.doi.org/10.1186/s12864-017-3676-8
|page=304-314
|pub_year=2017
|pdf=MolBiolEvol_Teufel_2018.pdf
|pdf=BMCGenomics_EcoliPTMs_2017.pdf
|link=https://academic.oup.com/mbe/article-lookup/doi/10.1093/molbev/msy210
|comment = [https://doi.org/10.1101/366971 bioRxiv preprint] (deposited July 10, 2018)
|pubmed=30428072
}}
}}
<li value="172"> {{Paper
</li>
|title=Comprehensive de novo peptide sequencing from MS/MS pairs generated through complementary collision induced dissociation and 351 nm ultraviolet photodissociation
<li value="186"> {{Paper
|authors=AP Horton, SA Robotham, JR Cannon, DD Holden, EM Marcotte, Brodbelt JS
|title=Photography Coupled with Self-Propagating Chemical Cascades. The Differentiation and Quantitation of G and V Nerve Agent Mimics via Chromaticity
|journal=Analytical Chemistry
|authors=Sun X, Boulgakov AA, Smith L, Metola P, Marcotte EM, Anslyn EV
|pubmed=28234449
|journal=ACS Central Science
|volume=89(6)
|volume=4(7)
|page=3747–3753
|page=854-861
|link=http://dx.doi.org/10.1021/acs.analchem.7b00130
|pubmed=30062113
|pub_year=2017
|pub_year=2018
|pdf=AnalyticalChemistry_UVnovo2_2017.pdf
|pdf=ACSCentralScience_LegoNerveGas_2018.pdf
|link=https://pubs.acs.org/doi/10.1021/acscentsci.8b00193
}}
}}
<li value="171"> {{Paper
</li>
|title=WheatNet: A genome-scale functional network for hexaploid bread wheat, ''Triticum aestivum''
<li value="185"> {{Paper
|authors=Lee T, Hwang S, Kim CY, Shim H, Kim H, Ronald PC, Marcotte EM, Lee I
|title=Classification of single particles from human cell extract reveals distinct structures
|journal=Molecular Plant
|authors=Verbeke EJ, Mallam AL, Drew K, Marcotte EM, Taylor DW
|pubmed=28450181
|journal=Cell Reports
|volume=S1674-2052(17)
|volume=(24)1
|page=30108-9
|page=259–268.e3
|link=http://dx.doi.org/10.1016/j.molp.2017.04.006
|link=https://doi.org/10.1016/j.celrep.2018.06.022
|pdf=MolPlant_WheatNet_2017.pdf
|pubmed=29972786
|pub_year=2017
|pdf=CellReports_ShotgunEM_2018.pdf
|comment = [http://dx.doi.org/10.1101/105098 bioRxiv preprint (deposited February 6, 2017)]
|pub_year=2018
|comment = [https://www.biorxiv.org/content/early/2018/01/14/247254 bioRxiv preprint] (deposited January 14 , 2018)
}}
}}
<li value="170"> {{Paper
</li>
|title=Murine Cytomegalovirus Deubiquitinase Regulates Viral Chemokine Levels To Control Inflammation and Pathogenesis
<li value="184"> {{Paper
|authors=Hilterbrand AT, Boutz DR, Marcotte EM, Upton JW
|title=Single-step precision genome editing in yeast using CRISPR-Cas9   
|journal=mBio
|authors= Akhmetov A, Laurent JM, Gollihar J, Gardner EC, Garge RK, Ellington AD, Kachroo AH, Marcotte EM  
|pubmed=28096485
|journal=Bio-protocol
|volume=8
|volume=8(6)
|page=e01864-16
|page=e2765
|link=http://dx.doi.org/10.1128/mBio.01864-16
|pubmed=29770349
|pub_year=2017
|pub_year=2018
|pdf=mBio_CMBdeubiquitinase_2017.pdf
|pdf=Bio-protocol_YeastCRISPR_2018.pdf
|link=http://dx.doi.org/10.21769/BioProtoc.2765
}}
}}
</li>
</li>
</ol>
<li value="183"> {{Paper
 
|title=Protein localization screening in vivo reveals novel regulators of multiciliated cell development and function
== 2016 ==
|authors=Tu F, Sedzinski J, Ma Y, Marcotte EM, Wallingford JB
<ol>
|journal=J Cell Sci
<li value="169"> {{Paper
|volume=131 (3)
|title=Computational Discovery of Pathway-Level Genetic Vulnerabilities in Non-Small-Cell Lung Cancer
|page=jcs206565
|authors=Young JH, Peyton M, Kim HS, McMillan E, Minna JD, White MA, Marcotte EM
|pubmed=29180514
|journal=Bioinformatics
|pub_year=2018
|pubmed=26755624
|pdf=JCellSci_CiliaScreen_2018.pdf
|volume=32(9)
|link=http://jcs.biologists.org/content/131/3/jcs206565
|link=http://dx.doi.org/10.1093/bioinformatics/btw010
|comment=[[File:JCSCiliaCover2018.jpg||100px|right]]
|page=1373-9
|pdf=Bioinformatics_LungCancer_2016.pdf
|comment = [https://bitbucket.org/youngjh/nsclc_paper Supporting code]
|pub_year=2016
}}
}}
<li value="168"> {{Paper
</li>
|title=Molecular-level analysis of the serum antibody repertoire in young adults before and after seasonal influenza vaccination
</ol>
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|journal=Nature Medicine
== 2017 ==
|pubmed=27820605
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|pdf=NatureMedicine_FluIgGSeq_2016.pdf
|authors=Hernandez ET, Swaminathan J, Marcotte EM , Anslyn EV
|link=http://dx.doi.org/10.1038/nm.4224
|journal=New Journal of Chemistry
|comment=[[File:NatureMedicineIgSeqCover2016.jpg||100px|right]]
|pubmed=
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<li value="167"> {{Paper
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|title=Genome evolution in the allotetraploid frog ''Xenopus laevis''
<li value="181"> {{Paper
|authors=Session AM*, Uno Y*, Kwon T*, et al.
|title=Identifying direct contacts between protein complex subunits from their conditional dependence in proteomics datasets
|journal=Nature
|authors=Drew K, Müller CL, Bonneau R, Marcotte EM
|pubmed=27762356
|journal=PLoS Computational Biology
|volume=538
|volume=13(10)
|page=336–343
|page=e1005625
|pdf=Nature_XenopusGenome_2016.pdf
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|pub_year=2017
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<li value="166"> {{Paper
</li>
|title=Temporal Stability and Molecular Persistence of the Bone Marrow Plasma Cell Antibody Repertoire
<li value="180"> {{Paper
|authors=Wu GC, Cheung NV, Georgiou G, Marcotte EM, Ippolito GC
|title=Metabolic crosstalk regulates ''Porphyromonas gingivalis'' colonization and virulence during oral polymicrobial infection
|journal=Nature Communications
|authors=Kuboniwa M, Houser JR, Hendrickson EL, Wang Q, Alghamdi SA, Sakanaka A, Miller DP, Hutcherson JA, Wang T, Beck DAC, Whiteley M, Amano A, Wang H, Marcotte EM, Hackett M, Lamont RJ
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|journal=Nature Microbiology
|volume=7
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|page=1493–1499
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|pub_year=2016
|pdf=NatureMicrobiology_PolymicrobialInfection_2017.pdf
|comment = [http://dx.doi.org/10.1101/066878 bioRxiv preprint (deposited August 2, 2016)]
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<li value="165"> {{Paper
</li>
|title=The ciliopathy-associated CPLANE proteins direct basal body recruitment of intraflagellar transport machinery
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|title=Systematic bacterialization of yeast genes identifies a near-universally swappable pathway
|journal=Nature Genetics
|authors=Kachroo AH, Laurent JM, Akhmetov A, Szilagyi-Jones M, McWhite CD, Zhao A, Marcotte EM
|pubmed=27158779
|journal=eLife
|volume=48(6)
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|link=http://dx.doi.org/10.1038/ng.3558
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<li value="164"> {{Paper
</li>
|title=Predicting Drug Synergy and Antagonism from Genetic Interaction Neighborhoods
<li value="178"> {{Paper
|authors=Young JH, Marcotte EM
|title=A highly parallel strategy for storage of digital information in living cells
|journal=bioRxiv
|authors=Akhmetov A, Ellington A, Marcotte E
|pubmed=
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|volume=
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<li value="163"> {{Paper
</li>
|title=Predictability of Genetic Interactions from Functional Gene Modules
<li value="177"> {{Paper
|authors=Young JH, Marcotte EM
|title=Systems-wide studies uncover Commander, a multiprotein complex essential to human development
|journal=G3
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|pubmed=28007839
|journal=Cell Systems
|volume=7
|volume=4
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|page=483-494
|link=http://www.g3journal.org/content/early/2016/12/19/g3.116.035915.abstract
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<li value="162"> {{Paper
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|title=Sperm is epigenetically programmed to regulate gene transcription in embryos
<li value="176"> {{Paper
|authors=Teperek M, Simeone A, Gaggioli V, Miyamoto K, Allen G, Erkek S, Peters A, Kwon T, Marcotte E, Zegerman P, Bradshaw C, Gurdon J, Jullien J
|title=Integration of over 9,000 mass spectrometry experiments builds a global map of human protein complexes
|journal=Genome Research
|authors=Drew, K., Lee, C., Huizar, R. L., Tu, F., Borgeson, B., McWhite, C. D., Ma, Y., Wallingford, J. B., Marcotte, E. M.
|pubmed=27034506
|journal=Molecular Systems Biology
|volume=26
|page=932
|pdf=GenomeResearch_SpermEpigenetics_2016.pdf
|volume=13
|page=1034-1046
|pubmed=28596423
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|pdf=MolecularSystemsBiology_2017_HuMap.pdf
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|pub_year=2017
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}}
<li value="161"> {{Paper
</li>
|title=Towards Consensus Gene Ages
<li value="175"> {{Paper
|authors=Liebeskind BJ, McWhite CD, Marcotte EM
|title=GWAB: a web server for the network-based boosting of human genome-wide association data
|journal=Genome Biology and Evolution
|authors=Shim JE, Bang C, Yang S, Lee T, Hwang S, Kim CY, Singh-Blom UM, Marcotte EM, Lee I
|pubmed=27259914
|journal=Nucleic Acids Research
|volume=8(6)
|pubmed=28449091
|pdf=GenomeBiolEvol_ConsensusGeneAges_2016.pdf
|volume=89(6)
|link=http://dx.doi.org/10.1093/gbe/evw113
|page=3747–3753
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|comment = [http://biorxiv.org/content/early/2016/03/01/042036 bioRxiv preprint (deposited March 1)] [https://github.com/marcottelab/Gene-Ages Supporting code and datasets]
|pub_year=2017
|pub_year=2016
|pdf=NAR_GWAB_2017.pdf
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}}
<li value="160"> {{Paper
</li>
|title=UVnovo: A de Novo Sequencing Algorithm Using Single Series of Fragment Ions via Chromophore Tagging and 351 nm Ultraviolet Photodissociation Mass Spectrometry
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|authors=Robotham SA, Horton AP, Cannon JR, Cotham VC, Marcotte EM, Brodbelt JS
|title=The ''E. coli'' molecular phenotype under different growth conditions
|journal=Analytical Chemistry
|authors=Caglar MU, Houser JR, Barnhart CS, Boutz DR, Carroll SM, Dasgupta A, Lenoir WF, Smith BL, Sridhara V, Sydykova DK, Vander Wood D, Marx CJ, Marcotte EM, Barrick JE, Wilke CO
|pubmed=26938041
|journal=Scientific Reports
|volume=88(7)
|pubmed=28417974
|pdf=AnalyticalChemistry_UVnovo_2016.pdf
|volume=7
|link=http://pubs.acs.org/doi/abs/10.1021/acs.analchem.6b00261
|page=45303
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|pub_year=2017
|pub_year=2016
|pdf=ScientificReports_EcoliMolecularPhenotype_2017.pdf
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}}
</li>
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</ol>
<li value="173"> {{Paper
 
|title=Large-scale analysis of post-translational modifications in ''E. coli'' under glucose-limiting conditions
== 2015 ==
|authors=Brown CW, Sridhara V, Boutz DR, Person MD, Marcotte EM, Barrick JE, Wilke CO
<ol>
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<li value="159"> {{Paper
|pubmed=28412930
|title=Interrogating conserved elements of diseases using Boolean combinations of orthologous phenotypes
|volume=18(1)
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|page=301
|journal=bioRxiv
|link=http://dx.doi.org/10.1186/s12864-017-3676-8
|pub_year=2015
|pub_year=2017
|volume=posted April 13
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|title=Comprehensive de novo peptide sequencing from MS/MS pairs generated through complementary collision induced dissociation and 351 nm ultraviolet photodissociation
|journal=Data in Brief
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|pubmed=26870755
|journal=Analytical Chemistry
|volume=6
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|title=WheatNet: A genome-scale functional network for hexaploid bread wheat, ''Triticum aestivum''
|journal=Nucl. Acid. Res.
|authors=Lee T, Hwang S, Kim CY, Shim H, Kim H, Ronald PC, Marcotte EM, Lee I
|pubmed=26527726
|journal=Molecular Plant
|volume=44(D1)
|pubmed=28450181
|link=http://dx.doi.org/10.1093/nar/gkv1155
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|pub_year=2015
|pdf=MolPlant_WheatNet_2017.pdf
|pub_year=2017
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}}
<li value="156"> {{Paper
</li>
|title=Intrinsic antimicrobial resistance determinants in the 'superbug' P. aeruginosa
<li value="170"> {{Paper
|authors=Murray J, Kwon T, Marcotte EM, Whiteley M
|title=Murine Cytomegalovirus Deubiquitinase Regulates Viral Chemokine Levels To Control Inflammation and Pathogenesis
|authors=Hilterbrand AT, Boutz DR, Marcotte EM, Upton JW
|journal=mBio
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|pubmed=26507235
|pubmed=28096485
|volume=6(6)
|volume=8
|link=http://dx.doi.org/10.1128/mBio.01603-15
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|journal=Nature Communications
== 2016 ==
|pubmed=26648521
<ol>
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<li value="169"> {{Paper
|volume=6
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|page=Article #8885
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}}
<li value="154"> {{Paper
</li>
|title=Systematic comparison of variant calling pipelines using gold standard personal exome variants
<li value="168"> {{Paper
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|title=Molecular-level analysis of the serum antibody repertoire in young adults before and after seasonal influenza vaccination
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|journal=Nature Medicine
|volume=5
|pubmed=27820605
|link=http://dx.doi.org/10.1038/srep17875
|volume=22(12)
|comment=[http://www.marcottelab.org/paper-pdfs/VariantCallingParameterSettings.txt Example variant calling parameters] [http://www.marcottelab.org/paper-pdfs/BEDsandGoldstandardVCFs.zip Gold standard vcf and exome capture region bed files]
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|pdf=NatureMedicine_FluIgGSeq_2016.pdf
|pdf=ScientificReports_Variants_2015.pdf
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|pub_year=2015
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|pub_year=2016
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}}
<li value="153"> {{Paper
</li>
|title=Efforts to make and apply humanized yeast
<li value="167"> {{Paper
|authors=Laurent JM, Young JH, Kachroo AH, Marcotte EM
|title=Genome evolution in the allotetraploid frog ''Xenopus laevis''
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|pub_year=2015
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<li value="152"> {{Paper
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|pubmed=27762356
|volume=525
|volume=538
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|pdf=Nature_XenopusGenome_2016.pdf
|pdf=Nature_AnimalComplexes_2015.pdf
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|comment=[http://www.nature.com/nature/journal/v538/n7625/full/538320a.html News&Views] and [http://www.marcottelab.org/paper-pdfs/Nature_XenopusGenome_NewsAndViews_2016.pdf pdf]; [http://www.marcottelab.org/paper-pdfs/Nature_XenopusGenome_2016_SupplementIncludesFunding.pdf Supplementary Information] [[File:NatureXenopusCover2016.jpg||100px|right]]
|pub_year=2015
|pub_year=2016
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}}
<li value="151"> {{Paper
</li>
|title=Applications of comparative evolution to human disease genetics
<li value="166"> {{Paper
|authors=McWhite CD, Liebeskind BJ, Marcotte EM
|title=Temporal Stability and Molecular Persistence of the Bone Marrow Plasma Cell Antibody Repertoire
|journal=Current Opinion in Genetics & Development
|authors=Wu GC, Cheung NV, Georgiou G, Marcotte EM, Ippolito GC
|pubmed=26338499
|journal=Nature Communications
|volume=35
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|volume=7
|link=http://dx.doi.org/10.1016/j.gde.2015.08.004
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|pdf=COGD_comparativeevolution_2015.pdf
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|pub_year=2016
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<li value="150"> {{Paper
</li>
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|title=The ciliopathy-associated CPLANE proteins direct basal body recruitment of intraflagellar transport machinery
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|pub_year=2015
|pub_year=2016
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<li value="149"> {{Paper
</li>
|title=Systematic humanization of yeast genes reveals conserved functions and genetic modularity
<li value="164"> {{Paper
|authors=Kachroo AH, Laurent JM, Yellman CM, Meyer AG, Wilke CO, Marcotte EM  
|title=Predicting Drug Synergy and Antagonism from Genetic Interaction Neighborhoods
|journal=Science
|authors=Young JH, Marcotte EM
|pubmed=25999509
|journal=bioRxiv
|volume=348(6237)
|pubmed=
|page=921-925
|volume=
|link=http://www.sciencemag.org/content/348/6237/921.abstract.html
|link=http://dx.doi.org/10.1101/050567
|pdf=Science_HumanizedYeast_2015.pdf
|page=deposited April 27
|comment=[http://www.marcottelab.org/paper-pdfs/Science_HumanizedYeast_2015_SupplementaryMaterials.pdf Supplement] [http://www.sciencemag.org/content/348/6237/921/suppl/DC1 Supplementary Tables and Files] Science magazine supplies a direct link around their paywall for free access to the [http://www.sciencemag.org/cgi/content/full/348/6237/921?ijkey=Bbngd7YBvhX9s&keytype=ref&siteid=sci  manuscript] and [http://www.sciencemag.org/cgi/rapidpdf/348/6237/921?ijkey=Bbngd7YBvhX9s&keytype=ref&siteid=sci pdf reprint]. Code and data for protein interaction evolution simulations are [https://github.com/wilkelab/complex_divergence_simul here]
|pub_year=2016
|pub_year=2015
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<li value="148"> {{Paper
</li>
|title=Modes of Interaction between Individuals Dominate the Topologies of Real World Networks
<li value="163"> {{Paper
|authors=Lee I, Kim E, Marcotte EM
|title=Predictability of Genetic Interactions from Functional Gene Modules
|journal=PLoS One
|authors=Young JH, Marcotte EM
|pubmed=25793969
|journal=G3
|volume=10(3)
|pubmed=28007839
|page=e0121248
|volume=7
|link=http://dx.doi.org/10.1371/journal.pone.0121248
|pdf=G3_GeneticInteractions_2017.pdf
|pdf=PLoSOne_NetworkTopology_2015.pdf
|link=http://www.g3journal.org/content/early/2016/12/19/g3.116.035915.abstract
|pub_year=2015
|page=617-624
|pub_year=2016
|comment = [http://dx.doi.org/10.1101/049627 bioRxiv preprint (deposited April 25, 2016)]
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<li value="147"> {{Paper
</li>
|title=The DEAH-box helicase Dhr1 dissociates U3 from the pre-rRNA to promote folding the central pseudoknot
<li value="162"> {{Paper
|authors=Sardana R, Liu X, Granneman S, Zhu J, Gill M, Papoulas O, Marcotte EM, Tollervey D, Correll CC, Johnson AW
|title=Sperm is epigenetically programmed to regulate gene transcription in embryos
|journal=PLoS Biology
|authors=Teperek M, Simeone A, Gaggioli V, Miyamoto K, Allen G, Erkek S, Peters A, Kwon T, Marcotte E, Zegerman P, Bradshaw C, Gurdon J, Jullien J
|pubmed=25710520
|journal=Genome Research
|volume=13(2)
|pubmed=27034506
|page=e1002083
|volume=26
|pdf=PLoSBiology_DHR1_2015.pdf
|pdf=GenomeResearch_SpermEpigenetics_2016.pdf
|link=http://dx.doi.org/10.1371/journal.pbio.1002083
|page=1034-1046
|pub_year=2015
|link=http://dx.doi.org/10.1101/gr.201541.115
|pub_year=2016
}}
}}
<li value="146"> {{Paper
</li>
|title=A self-assembling lanthanide molecular nanoparticle for optical imaging
<li value="161"> {{Paper
|authors=Brown KA, Yang X, Schipper D, Hall JW, DePue LJ, Gnanam AJ, Arambula JF, Jones JN, Swaminathan J, Dieye Y, Vadivelu J, Chandler DJ, Marcotte EM, Sessler JL, Ehrlich LIR, Jones RA
|title=Towards Consensus Gene Ages
|journal=Dalton Transactions
|authors=Liebeskind BJ, McWhite CD, Marcotte EM
|pubmed=25512085
|journal=Genome Biology and Evolution
|volume=44(6)
|pubmed=27259914
|page=2667-75
|volume=8(6)
|pub_year=2015
|pdf=GenomeBiolEvol_ConsensusGeneAges_2016.pdf
|link=http://dx.doi.org/10.1039/c4dt02646b
|link=http://dx.doi.org/10.1093/gbe/evw113
|pdf=DaltonTransactions_LanthanideNanoparticle_2015.pdf
|page=1812-23
|comment = [http://biorxiv.org/content/early/2016/03/01/042036 bioRxiv preprint (deposited March 1)] [https://github.com/marcottelab/Gene-Ages Supporting code and datasets]
|pub_year=2016
}}
}}
</li>
</li>
</ol>
<li value="160"> {{Paper
 
|title=UVnovo: A de Novo Sequencing Algorithm Using Single Series of Fragment Ions via Chromophore Tagging and 351 nm Ultraviolet Photodissociation Mass Spectrometry
== 2014 ==
|authors=Robotham SA, Horton AP, Cannon JR, Cotham VC, Marcotte EM, Brodbelt JS
|journal=Analytical Chemistry
|pubmed=26938041
|volume=88(7)
|pdf=AnalyticalChemistry_UVnovo_2016.pdf
|link=http://pubs.acs.org/doi/abs/10.1021/acs.analchem.6b00261
|page=3990-7
|comment = [https://github.com/marcottelab/UVnovo Supporting code]
|pub_year=2016
}}
</li>
</ol>
 
== 2015 ==
<ol>
<ol>
<li value="145"> {{Paper
<li value="159"> {{Paper
|title= A theoretical justification for single molecule peptide sequencing
|title=Interrogating conserved elements of diseases using Boolean combinations of orthologous phenotypes
|authors=Swaminathan J, Boulgakov AA, Marcotte EM
|authors=Woods JO, Tien M, Marcotte EM
|journal=PLoS Computational Biology
|journal=bioRxiv
|pubmed=25714988
|pub_year=2015
|volume=11(2)
|volume=posted April 13
|page=e1004080
|page=
|link=http://dx.doi.org/10.1371/journal.pcbi.1004080
|link=https://www.biorxiv.org/content/10.1101/017947v1
|pdf=PLoSComputationalBiology_SingleMoleculeProteomics_2015.pdf
|comment=[http://dx.doi.org/10.1101/010587 bioRxiv preprint]
|pub_year=2014 bioRxiv, 2015 PLoS CB
}}
}}
<li value="144"> {{Paper
</li>
|title=Lanthanide  nano-drums:  A  new  class  of molecular  nanoparticles  for potential biomedical applications
<li value="158"> {{Paper
|authors=Jones RA, Gnanam AJ, Arambula JF, Jones JN, Swaminathan J, Yang X, Schipper D, Hall JW, DePue LJ, Dieye Y, Vadivelu J, Chandler DJ, Marcotte EM, Sessler JL, Ehrlich LIR, Brown KA
|title=Proteome-wide dataset supporting the study of ancient metazoan macromolecular complexes
|journal=Faraday Discussions
|authors=Phanse S, Wan C, Borgeson B, Tu F, Drew K, Clark G, Xiong X, Kagan O, Kwan J, Bezginov A, Chessman K, Pal S, Cromar G, Papoulas O, Ni Z, Boutz DR, Stoilova S, Havugimana PC, Guo X, Malty RH, Sarov M, Greenblatt J, Babu M, Derry WB, R Tillier E, Wallingford JB, Parkinson J, Marcotte EM, Emili A
|pubmed=25284181
|journal=Data in Brief
|volume=175
|pubmed=26870755
|page=241-55
|volume=6
|link=http://dx.doi.org/10.1039/C4FD00117F
|link=http://dx.doi.org/10.1016/j.dib.2015.11.062
|pub_year=2014
|page=715-21
|pdf=FaradayDiscussions_LanthanideNanodrums_2014.pdf
|pub_year=2015
|pdf=Data_In_Brief_AnimalComplexes_2016.pdf
}}
}}
<li value="143"> {{Paper
</li>
|title=Identifying direct targets of transcription factor Rfx2 that coordinate ciliogenesis and cell movement
<li value="157"> {{Paper
|authors=Kwon T, Chung M-I, Gupta R, Baker JC, Wallingford JB, Marcotte EM
|title=MouseNet v2: A database of gene networks for studying the laboratory mouse and eight other model vertebrates
|journal=Genomics Data
|authors=Kim E, Hwang S, Kim H, Shim H, Kang B, Yang S, Shim JH, Shin SY, Marcotte EM, Lee I
|pubmed=25419512
|journal=Nucl. Acid. Res.
|volume=2
|pubmed=26527726
|page=192-194
|volume=44(D1)
|link=http://www.sciencedirect.com/science/article/pii/S2213596014000488
|link=http://dx.doi.org/10.1093/nar/gkv1155
|pub_year=2014
|page=D848-54
|pdf=GenomicsData_RFX2_2014.pdf
|pdf=NAR_MouseNet2_2015.pdf
|pub_year=2015
}}
}}
<li value="142"> {{Paper
</li>
|title=MORPHIN: a web tool for human disease research by projecting model organism biology onto a human integrated gene network
<li value="156"> {{Paper
|authors=Hwang S, Kim E, Yang S, Marcotte EM, Lee I
|title=Intrinsic antimicrobial resistance determinants in the 'superbug' P. aeruginosa
|journal=Nucleic Acids Research
|authors=Murray J, Kwon T, Marcotte EM, Whiteley M
|pubmed=24861622
|journal=mBio
|volume=42(Web Server issue)
|pubmed=26507235
|page=W147-53
|volume=6(6)
|link=http://dx.doi.org/10.1093/nar/gku434
|link=http://dx.doi.org/10.1128/mBio.01603-15
|pub_year=2014
|page=e01603-15
|pdf=NAR_MORPHIN_2014.pdf
|pdf=mBio_Murray_2015.pdf
|pub_year=2015
}}
}}
<li value="141"> {{Paper
</li>
|title=Protein-to-mRNA ratios are conserved between <i>Pseudomonas aeruginosa</i> strains
<li value="155"> {{Paper
|authors=Kwon T, Huse HK, Vogel C, Whiteley M, Marcotte EM
|title=Long-term neural and physiological phenotyping of a single human
|journal=Journal of Proteome Research
|authors=Poldrack RA, Laumann T, Koyejo O, Gregory B, Hover A, Chen M-Y, Luci J, Huk A, Joo S-J, Boyd R, Hunicke-Smith S, Simpson ZB, Caven T, Sochat V, Shine JM, Gordon E, Snyder AZ, Adeyemo B, Petersen SE, Glahn D, Mckay DR, Blangero J, Frick L, Marcotte EM, Mumford JA
|pubmed=24742327
|journal=Nature Communications
|pdf=JProteomeResearch_Pseudomonas_2014.pdf
|pubmed=26648521
|volume=13(5)
|pdf=NatureCommunications_Poldrackome_2015.pdf
|page=2370-80
|volume=6
|link=http://pubs.acs.org/doi/abs/10.1021/pr4011684
|link=http://dx.doi.org/10.1038/ncomms9885
|pub_year=2014
|page=Article #8885
|pub_year=2015
}}
}}
<li value="140"> {{Paper
</li>
|title=Proteomic identification of monoclonal antibodies from serum
<li value="154"> {{Paper
|authors=Boutz DR, Horton AP, Wine Y, Lavinder JJ, Georgiou G, Marcotte EM
|title=Systematic comparison of variant calling pipelines using gold standard personal exome variants
|journal=Analytical Chemistry
|authors=Hwang S, Eiru K, Lee I, Marcotte EM
|pubmed=24684310
|journal=Scientific Reports
|volume=86(10)
|pubmed=26639839
|page=4758-66
|volume=5
|pdf=AnalyticalChemistry_IgGProteomics_2014.pdf
|link=http://dx.doi.org/10.1038/srep17875
|link=http://pubs.acs.org/doi/abs/10.1021/ac4037679
|comment=[http://www.marcottelab.org/paper-pdfs/VariantCallingParameterSettings.txt Example variant calling parameters] [http://www.marcottelab.org/paper-pdfs/BEDsandGoldstandardVCFs.zip Gold standard vcf and exome capture region bed files]
|pub_year=2014
|page=17875
|pdf=ScientificReports_Variants_2015.pdf
|pub_year=2015
}}
}}
<li value="139"> {{Paper
</li>
|title=Formation of intracellular glutamine synthetase bodies depends strongly upon cellular age and glucose availability
<li value="153"> {{Paper
|authors=O’Connell JD, Tsechansky M, West-Driga M, Marcotte EM
|title=Efforts to make and apply humanized yeast
|journal=PeerJ PrePrints
|authors=Laurent JM, Young JH, Kachroo AH, Marcotte EM
|pubmed=
|journal=Briefings in Functional Genomics
|pdf=PeerJPreprints_GSBodies_2014.pdf
|pubmed=26462863
|volume=2
|volume=15(2)
|page=e270v1
|link=http://dx.doi.org/10.1093/bfgp/elv041
|link=http://dx.doi.org/10.7287/peerj.preprints.270v1
|page=155-63
|pub_year=2014
|pdf=BriefingsInFunctionalGenomics_HumanizedYeast_2015.pdf
|pub_year=2015
}}
}}
</li>
</li>
<li value="138"> {{Paper
<li value="152"> {{Paper
|title=A proteomic survey of widespread protein aggregation in yeast
|title=Panorama of ancient metazoan macromolecular complexes
|authors=O’Connell JD, Tsechansky M, Royall A, Boutz DR, Ellington AD, Marcotte EM
|authors=Wan C, Borgeson B, Phanse S, Tu F, Drew K, Clark G, Xiong X, Kagan O, Kwan J, Bezginov A, Chessman K, Pal S, Cromar G, Papoulas O, Ni Z, Boutz DR, Stoilova S, Havugimana PC, Guo X, Malty RH, Sarov M, Greenblatt J, Babu M, Derry WB, R Tillier E, Wallingford JB, Parkinson J, Marcotte EM, Emili A
|journal=Molecular BioSystems
|journal=Nature
|pubmed=24488121
|pubmed=26344197
|volume=10
|volume=525
|pdf=MolecularBioSystems_Aggregates_2014.pdf
|page=339–344
|page=851-861
|link=http://dx.doi.org/10.1038/nature14877
|link=http://dx.doi.org/10.1039/C3MB70508K
|pdf=Nature_AnimalComplexes_2015.pdf
|pub_year=2014
|comment=Supplementary data is available [http://www.nature.com/nature/journal/vaop/ncurrent/full/nature14877.html#supplementary-information here]. [http://metazoa.med.utoronto.ca/ Supporting web site]
|comment=[http://www.marcottelab.org/paper-pdfs/MolecularBioSystems_Aggregates_2014_SupplementalTables.pdf Supplement] [http://marcottelab.org/index.php/Widespreadaggregation.2013 Supporting Datasets]
|pub_year=2015
}}
}}
</li>
</li>
<li value="137"> {{Paper
<li value="151"> {{Paper
|title=Bacteriophages use an expanded genetic code on evolutionary paths to higher fitness
|title=Applications of comparative evolution to human disease genetics
|authors=Hammerling MJ, Ellefson JW, Boutz DR, Marcotte EM, Ellington AD, Barrick JE
|authors=McWhite CD, Liebeskind BJ, Marcotte EM
|journal=Nature Chemical Biology
|journal=Current Opinion in Genetics & Development
|pubmed=24487692
|pubmed=26338499
|volume=10(3)
|volume=35
|link=http://www.nature.com/nchembio/journal/vaop/ncurrent/full/nchembio.1450.html
|page=16–24
|pdf=NatureChemBio_Phage_2014.pdf
|link=http://dx.doi.org/10.1016/j.gde.2015.08.004
|comment=[http://www.marcottelab.org/paper-pdfs/NatureChemBio_Phage_2014-S1.pdf Supplement] [http://www.marcottelab.org/paper-pdfs/NatureChemBio_Phage_2014-S2.xlsx Supplemental Data 1] [http://www.marcottelab.org/paper-pdfs/NatureChemBio_Phage_2014-S3.xlsx Supplemental Data 2]
|pdf=COGD_comparativeevolution_2015.pdf
|page=178-80
|comment=COGD supplies a direct link around their paywall for [http://authors.elsevier.com/a/1ReqI,LqAZ3H8k free access to the paper]
|pub_year=2014
|pub_year=2015
}}
}}
</li>
</li>
<li value="136"> {{Paper
<li value="150"> {{Paper
|title=Yeast cells expressing the human mitochondrial DNA polymerase reveal correlations between polymerase fidelity and human disease progression
|title=Controlled Measurement and Comparative Analysis of Cellular Components in E. coli Reveals Broad Regulatory Changes in Response to Glucose Starvation
|authors=Qian Y, Kachroo A, Yellman CM, Marcotte EM, Johnson KA
|authors=Houser JR, Barnhart C, Boutz DR, Carroll SM, Dasgupta A, Michener JK, Needham BD, Papoulas O, Sridhara V, Sydykova DK, Marx CJ, Trent MS, Barrick JE, Marcotte EM, Wilke CO
|journal=Journal of Biological Chemistry
|journal=PLoS Computational Biology
|pubmed=24398692
|pubmed=26275208
|volume=289
|volume=11(8)
|pdf=JBiolChem_hPOLG_2014.pdf
|page=e1004400
|page=5970-5985
|link=http://dx.doi.org/10.1371/journal.pcbi.1004400
|link=http://dx.doi.org/10.1074/jbc.M113.526418
|pdf=PLoSComputationalBiology_GlucoseStarvation_2015.pdf
|pub_year=2014
|pub_year=2015
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}}
</li>
</li>
<li value="135"> {{Paper
<li value="149"> {{Paper
|title=Identification and characterization of the constituent human serum antibodies elicited by vaccination
|title=Systematic humanization of yeast genes reveals conserved functions and genetic modularity
|authors=Lavinder JJ, Wine Y, Giesecke C, Ippolito GC, Horton AP, Lungu OI, Hoi KH, Dekosky BJ, Murrin EM, Wirth MM, Ellington AD, Dörner T, Marcotte EM, Boutz DR, Georgiou G
|authors=Kachroo AH, Laurent JM, Yellman CM, Meyer AG, Wilke CO, Marcotte EM  
|journal=Proc Natl Acad Sci USA
|journal=Science
|pubmed=24469811
|pubmed=25999509
|volume=111(6)
|volume=348(6237)
|page=2259-64
|page=921-925
|pdf=PNAS_Tetanus_2014.pdf
|link=http://www.sciencemag.org/content/348/6237/921.abstract.html
|pub_year=2014
|pdf=Science_HumanizedYeast_2015.pdf
|link=http://www.pnas.org/content/early/2014/01/23/1317793111.abstract
|comment=[http://www.marcottelab.org/paper-pdfs/Science_HumanizedYeast_2015_SupplementaryMaterials.pdf Supplement] [http://www.sciencemag.org/content/348/6237/921/suppl/DC1 Supplementary Tables and Files] Science magazine supplies a direct link around their paywall for free access to the [http://www.sciencemag.org/cgi/content/full/348/6237/921?ijkey=Bbngd7YBvhX9s&keytype=ref&siteid=sci  manuscript] and [http://www.sciencemag.org/cgi/rapidpdf/348/6237/921?ijkey=Bbngd7YBvhX9s&keytype=ref&siteid=sci pdf reprint]. Code and data for protein interaction evolution simulations are [https://github.com/wilkelab/complex_divergence_simul here]
|pub_year=2015
}}
}}
</li>
</li>
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<li value="148"> {{Paper
|title=Revisiting and revising the purinosome
|title=Modes of Interaction between Individuals Dominate the Topologies of Real World Networks
|authors=Zhao A, Tsechansky M, Ellington AD, Marcotte EM
|authors=Lee I, Kim E, Marcotte EM
|journal=Molecular BioSystems
|journal=PLoS One
|pubmed=24413256
|pubmed=25793969
|volume=10(3)
|volume=10(3)
|link=http://dx.doi.org/10.1039/C3MB70397E
|page=e0121248
|page=369-74
|link=http://dx.doi.org/10.1371/journal.pone.0121248
|pdf=MolecularBioSystems_RevisitingPurinosome_2013.pdf
|pdf=PLoSOne_NetworkTopology_2015.pdf
|pub_year=2014
|pub_year=2015
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}}
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</li>
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<li value="147"> {{Paper
|title=Coordinated genomic control of ciliogenesis and cell movement by Rfx2
|title=The DEAH-box helicase Dhr1 dissociates U3 from the pre-rRNA to promote folding the central pseudoknot
|authors=Chung MI*, Kwon T*, Tu F, Brooks ER, Gupta R, Meyer M, Baker JC, Marcotte EM, Wallingford JB
|authors=Sardana R, Liu X, Granneman S, Zhu J, Gill M, Papoulas O, Marcotte EM, Tollervey D, Correll CC, Johnson AW
|journal=eLife
|journal=PLoS Biology
|pubmed=24424412
|pubmed=25710520
|pdf=eLife_RFX2_2014.pdf
|volume=13(2)
|volume=3
|page=e1002083
|page=e01439
|pdf=PLoSBiology_DHR1_2015.pdf
|link=http://dx.doi.org/10.7554/eLife.01439
|link=http://dx.doi.org/10.1371/journal.pbio.1002083
|pub_year=2014
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<li value="146"> {{Paper
 
|title=A self-assembling lanthanide molecular nanoparticle for optical imaging
== 2013 ==
|authors=Brown KA, Yang X, Schipper D, Hall JW, DePue LJ, Gnanam AJ, Arambula JF, Jones JN, Swaminathan J, Dieye Y, Vadivelu J, Chandler DJ, Marcotte EM, Sessler JL, Ehrlich LIR, Jones RA
<ol>
|journal=Dalton Transactions
<li value="132"> {{Paper
|pubmed=25512085
|title=Statistical approach to protein quantification
|volume=44(6)
|authors=Gerster S, Kwon T, Ludwig C, Matondo M, Vogel C, Marcotte E, Aebersold R, Bühlmann P
|page=2667-75
|journal=Mol Cell Proteomics
|pub_year=2015
|pubmed=24255132
|link=http://dx.doi.org/10.1039/c4dt02646b
|volume=13(2)
|pdf=DaltonTransactions_LanthanideNanoparticle_2015.pdf
|link=http://dx.doi.org/10.1074/mcp.M112.025445
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|title=<i>Pseudomonas aeruginosa</i> enhances production of a non-alginate exopolysaccharide during long-term colonization of the cystic fibrosis lung
 
|authors=Huse HK, Kwon T, Zlosnik JEA, Speert DP, Marcotte EM, Whiteley M
== 2014 ==
|journal=PLoS One
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|pubmed=24324811
<li value="145"> {{Paper
|volume=8(12)
|title= A theoretical justification for single molecule peptide sequencing
|page=e82621
|authors=Swaminathan J, Boulgakov AA, Marcotte EM
|pdf=PLoSOne_PsI_2013.pdf
|journal=PLoS Computational Biology
|link=http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0082621
|pubmed=25714988
|pub_year=2013
|volume=11(2)
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|pdf=PLoSComputationalBiology_SingleMoleculeProteomics_2015.pdf
|title=A bacteriophage tailspike domain promotes self-cleavage of a human membrane-bound transcription factor, the myelin regulatory factor MYRF
|comment=[http://dx.doi.org/10.1101/010587 bioRxiv preprint]
|authors=Li Z*, Park Y*, Marcotte EM
|pub_year=2014 bioRxiv, 2015 PLoS CB
|journal=PLoS Biology
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|link=http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001624
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|volume=11(8)
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|title=Prediction of gene-phenotype associations in humans, mice, and plants using phenologs
|title=Lanthanide  nano-drums:  A  new  class  of molecular  nanoparticles  for potential biomedical applications
|authors=Woods JO, Singh-Blom UM, Laurent JM, McGary KL, Marcotte EM
|authors=Jones RA, Gnanam AJ, Arambula JF, Jones JN, Swaminathan J, Yang X, Schipper D, Hall JW, DePue LJ, Dieye Y, Vadivelu J, Chandler DJ, Marcotte EM, Sessler JL, Ehrlich LIR, Brown KA
|journal=BMC Bioinformatics
|journal=Faraday Discussions
|pubmed=23800157
|pubmed=25284181
|page=203
|volume=175
|volume=14
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|link=http://dx.doi.org/10.1186/1471-2105-14-203
|link=http://dx.doi.org/10.1039/C4FD00117F
|pub_year=2013
|pub_year=2014
|pdf=BMCBioinformatics_Phenologs_2013.pdf
|pdf=FaradayDiscussions_LanthanideNanodrums_2014.pdf
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<li value="143"> {{Paper
|title=Prediction and validation of gene-disease associations using methods inspired by social network analyses
|title=Identifying direct targets of transcription factor Rfx2 that coordinate ciliogenesis and cell movement
|authors=Singh-Blom UM, Natarajan N, Tewari A, Woods JO, Dhillon IS, Marcotte EM
|authors=Kwon T, Chung M-I, Gupta R, Baker JC, Wallingford JB, Marcotte EM
|journal=PLoS One
|journal=Genomics Data
|pubmed=
|pubmed=25419512
|volume=8(5)
|volume=2
|page=e58977
|page=192-194
|pub_year=2013
|link=http://www.sciencedirect.com/science/article/pii/S2213596014000488
|pubmed=23650495
|pub_year=2014
|pdf=PLoSOne_Catapult_2013.pdf
|pdf=GenomicsData_RFX2_2014.pdf
|link=http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0058977
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<li value="142"> {{Paper
|title=The proteomic response to mutants of the ''Escherichia coli'' RNA degradosome
|title=MORPHIN: a web tool for human disease research by projecting model organism biology onto a human integrated gene network
|authors=Zhou L, Zhang AB, Wang R, Marcotte EM, Vogel C
|authors=Hwang S, Kim E, Yang S, Marcotte EM, Lee I
|journal=Molecular BioSystems
|journal=Nucleic Acids Research
|pubmed=
|pubmed=24861622
|link=http://dx.doi.org/10.1039/C3MB25513A
|volume=42(Web Server issue)
|volume=9
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|page=750-757
|link=http://dx.doi.org/10.1093/nar/gku434
|pdf=MolecularBioSystems_RNADegradosome_2013.pdf
|pub_year=2014
|pubmed=23403814
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<li value="141"> {{Paper
|title=Molecular deconvolution of the monoclonal antibodies that comprise the polyclonal serum response
|title=Protein-to-mRNA ratios are conserved between <i>Pseudomonas aeruginosa</i> strains
|authors=Wine Y, Boutz DR, Lavinder JJ, Miklos AE, Hughes RA, Hoi KH, Jung ST, Horton AP, Murrin EM, Ellington AD, Marcotte EM, Georgiou G
|authors=Kwon T, Huse HK, Vogel C, Whiteley M, Marcotte EM
|journal=Proc Natl Acad Sci USA
|journal=Journal of Proteome Research
|pubmed=23382245
|pubmed=24742327
|volume=110(8)
|pdf=JProteomeResearch_Pseudomonas_2014.pdf
|page=2993–2998
|volume=13(5)
|pdf=PNAS_IgGProfiling_2013.pdf
|page=2370-80
|pub_year=2013
|link=http://pubs.acs.org/doi/abs/10.1021/pr4011684
|link=http://www.pnas.org/content/early/2013/02/01/1213737110.abstract 
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<li value="125"> {{Paper
<li value="140"> {{Paper
|title=Transiently transfected purine biosynthetic enzymes form stress bodies
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}}
</li>
</li>
</ol>
<li value="118"> {{Paper
 
|title=Dynamic reorganization of metabolic enzymes into intracellular bodies 
== 2010 ==
|authors=O'Connell JD, Zhao A, Ellington AD, Marcotte EM
<ol>
|journal=Annual Review of Cell and Developmental Biology
 
|pubmed=23057741
<li value="103"> {{Paper
|volume=28
|title=Parallel evolution in <i>Pseudomonas aeruginosa</i> over 39,000 generations <i>in vivo</i>
|link=http://www.annualreviews.org/doi/abs/10.1146/annurev-cellbio-101011-155841
|authors=Huse HK, Kwon T, Zlosnik JEA, Speert DP, Marcotte EM, Whiteley M
|page=89-111
|journal=mBIO
|pub_year=2012
|pub_year=2010
|pdf=AnnRevCellDevBiol_OConnell_2012.pdf
|volume=1(4)
|pubmed=20856824
|pdf=mBIO_CFPseudomonas_2010.pdf
|link=http://mbio.asm.org/content/1/4/e00199-10
|page=e00199-10
|comment=[http://www.sciencenews.org/view/generic/id/63939/title/To_researchers%E2%80%99_surprise,_one_Pseudomonas_infection_is_much_like_the_next ScienceNews] [http://www.marcottelab.org/index.php/PSEAE_CF.2010 Supplement]
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</li>
</li>
<li value="102"> {{Paper
<li value="117"> {{Paper
|title=Characterising and predicting haploinsufficiency in the human genome
|title=Insights into the regulation of protein abundance from proteomic and transcriptomic analyses 
|authors=Huang N, Lee I, Marcotte EM, Hurles M
|authors=Vogel C, Marcotte EM
|journal=PLoS Genetics
|journal=Nature Reviews Genetics
|pub_year=2010
|pubmed=22411467
|volume=6(10)
|volume=13
|pdf=PLoSGenetics_Haploinsufficiency_2010.pdf
|link=http://dx.doi.org/10.1038/nrg3185
|link=http://dx.doi.org/10.1371/journal.pgen.1001154
|pdf=NatureReviewsGenetics_ProteinAbundanceRegulation_2012.pdf
|page=e1001154
|page=227-232
|pubmed=20976243
|pub_year=2012
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</li>
<li value="101"> {{Paper
<li value="116"> {{Paper
|title=Protein abundances are more conserved than mRNA abundances across diverse taxa
|title=Proteomic and protein interaction network analysis of human T lymphocytes during cell-cycle entry
|authors=Laurent J, Vogel C, Kwon T, Craig SA, Boutz DR, Huse HK, Nozue K, Walia H, Whiteley M, Ronald PC, Marcotte EM
|authors=Orr SJ, Boutz DR, Wang R, Chronis C, Lea NC, Thayaparan T, Hamilton E, Milewicz H, Blanc E, Mufti GJ, Marcotte EM, Thomas NSB
|journal=Proteomics
|journal=Molecular Systems Biology
|pub_year=2010
|pubmed=22415777
|volume=10
|volume=8
|pubmed=21089048
|pdf=MolecularSystemsBiology_TCellCycleEntry_2012.pdf
|pdf=Proteomics_ProteinVersusRNAConservation_2010.pdf
|link=http://www.nature.com/msb/journal/v8/n1/full/msb20125.html
|link=http://onlinelibrary.wiley.com/doi/10.1002/pmic.201000327/abstract
|comment=[http://www.nature.com/msb/journal/v8/n1/suppinfo/msb20125_S1.html Supplement] [http://www.marcottelab.org/paper-pdfs/MolecularSystemsBiology_TCellCycleEntry_2012_Reviews.pdf Reviewer comments]
|page=4209–4212
|page=573
|comment=[http://www.marcottelab.org/paper-pdfs/MProteomics_ProteinVersusRNAConservation_2010_Supplement.zip Supplement]
|pub_year=2012
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}}
</li>
</li>
<li value="100"> {{Paper
<li value="115"> {{Paper
|title=It's the machine that matters: predicting gene function and phenotype from protein networks
|title=RFX2 is broadly required for ciliogenesis during vertebrate development
|authors=Wang PI, Marcotte EM
|authors=Chung M-I, Peyrot S, LeBoeuf S, Park TJ, McGary KL, Marcotte EM, Wallingford JB
|journal=Journal of Proteomics
|journal=Developmental Biology
|pub_year=2010
|pubmed=22227339
|volume=73(11)
|volume=363(1)
|pubmed=20637909
|page=155-165
|pdf=JProteomics_GBAReview_2010.pdf
|link=http://dx.doi.org/10.1016/j.ydbio.2011.12.029
|link=http://dx.doi.org/10.1016/j.jprot.2010.07.005
|pdf=DevelopmentalBiology_RFX2_2012.pdf
|page=2277-89
|pub_year=2012
|comment=[http://www.marcottelab.org/paper-pdfs/DevelopmentalBiology_RFX2_2011_SOM.pdf Supplement]
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}}
</li>
</li>
<li value="99"> {{Paper
<li value="114"> {{Paper
|title=Sequence signatures and mRNA concentration can explain two-thirds of protein abundance variation in a human cell line
|title=Label-free quantitation using weighted spectral counting
|authors=Vogel C, de Sousa Abreu R, Ko D, Le S-Y, Shapiro BA, Burns SC, Sandhu D, Boutz DR, Marcotte EM, Penalva LO
|authors=Vogel C, Marcotte EM
|journal=Molecular Systems Biology
|journal=Methods in Molecular Biology: Quantitative Methods in Proteomics
|pub_year=2010
|pubmed=22665309
|pubmed=20739923
|pub_year=2012
|volume=6
|volume=Marcus, K., ed., Humana Press, vol. 893(3)
|page=article 400
|page=321-341
|pdf=MolecularSystemsBiology_2010_HumanProteomics.pdf
|link=http://www.springerlink.com/content/ll221655443866x8/#section=1079488&page=1
|link=http://www.nature.com/msb/journal/v6/n1/full/msb201059.html
|pdf=MethodsMolBioProteomics_VogelMarcotte_2012.pdf
|comment=[http://www.marcottelab.org/paper-pdfs/MolecularSystemsBiology_2010_HumanProteomics_Supplement.pdf Supplement] [http://www.marcottelab.org/paper-pdfs/MolecularSystemsBiology_2010_HumanProteomics_S1.xls Supplemental Data (Excel format)] [http://www.marcottelab.org/paper-pdfs/MolecularSystemsBiology_2010_HumanProteomics_Fig2SourceData.txt Fig 2 source data] [http://www.marcottelab.org/paper-pdfs/MolecularSystemsBiology_2010_HumanProteomics_Fig2SourceData.txt Fig 3A source data] [http://www.marcottelab.org/paper-pdfs/MolecularSystemsBiology_2010_HumanProteomics_Fig2SourceData.txt Fig 3B source data] [http://www.marcottelab.org/paper-pdfs/MolecularSystemsBiology_2010_HumanProteomics_NewsAndViews.pdf News and Views]
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</li>
</li>
<li value="98"> {{Paper
</ol>
|title=Defining the pathway of cytoplasmic maturation of the 60S ribosomal subunit
 
|authors=Lo K-Y, Li Z, Bussiere C, Bresson S, Marcotte EM, Johnson AW
== 2011 ==
|journal=Molecular Cell
<ol>
|pub_year=2010
<li value="113"> {{Paper
|volume=39(2)
|title=Genetic dissection of the biotic stress response using a genome-scale gene network for rice
|page=196-208
|authors=Lee I, Seo Y-S, Coltrane D, Hwang S, Oha T, Marcotte EM, Ronald PC
|pubmed=20670889
|journal=Proc Natl Acad Sci USA
|pdf=MolecularCell_60SBiogenesis_2010.pdf
|pubmed=22042862
|link=http://www.cell.com/molecular-cell/fulltext/S1097-2765(10)00459-4
|page=18548-18553
|comment=[http://www.marcottelab.org/paper-pdfs/MolecularCell_60SBiogenesis_2010_Supplement.pdf Supplement]
|link=http://www.pnas.org/cgi/doi/10.1073/pnas.1110384108
|pdf=PNAS_RiceNet_2011_withSupplement.pdf
|pub_year=2011
|volume=108(45)
|comment=[http://www.pnas.org/lookup/suppl/doi:10.1073/pnas.1110384108/-/DCSupplemental Supplement]
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<li value="97"> {{Paper
<li value="112"> {{Paper
|title=Predicting genetic modifier loci using functional gene networks
|title=Predicting gene-disease associations using multiple species data
|authors=Lee I, Lehner B, Vavouri T, Shin J, Fraser AG, Marcotte EM
|authors=Natarajan N, Blom UM, Tewari A, Woods JO, Dhillon IS, Marcotte EM
|journal=Genome Research
|journal=UTCS Technical Report
|pub_year=2010
|pubmed=
|volume=20
|page=
|page=1143-1153
|pdf=TechnicalReport-PhenoNets-TR-2053.pdf
|pubmed=20538624
|link=http://apps.cs.utexas.edu/tech_reports/ncstrl/ncstrl2html.php?what=TR%20Abstracts&when=2011#UTEXAS.CS//CS-TR-11-37
|pdf=GenomeResearch_GeneticModifiers_2010.pdf
|pub_year=2011
|link=http://dx.doi.org/10.1101/gr.102749.109
|volume=TR-11-37
|comment=[http://www.marcottelab.org/paper-pdfs/GenomeResearch_GeneticModifiers_2010_SOM.pdf Supplement] [http://www.nature.com/nrg/journal/vaop/ncurrent/full/nrg2836.html Nature Reviews Genetics]
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<li value="96"> {{Paper
<li value="111"> {{Paper
|title=Systematic discovery of nonobvious human disease models through orthologous phenotypes
|title=Global protein expression regulation under oxidative stress
|authors=McGary KL, Park TJ, Woods JO, Cha HJ, Wallingford JB, Marcotte EM
|authors=Vogel C, Silva GM, Marcotte EM
|journal=Proc Natl Acad Sci U S A
|journal=Molecular and Cellular Proteomics
|pub_year=2010
|pubmed=21933953
|volume=107(14)
|page=M111.009217
|page=6544-9
|link=http://dx.doi.org/10.1074/mcp.M111.009217
|pubmed=20308572
|pdf=MolecularCellularProteomics_OxidativeProteomics_2011.pdf
|link=http://www.pnas.org/cgi/doi/10.1073/pnas.0910200107
|pub_year=2011
|pdf=PNAS_Phenologs_2010.pdf
|volume=10(12)
|comment=[http://www.marcottelab.org/paper-pdfs/PNAS_Phenologs_2010_Supplement.pdf Supplement] [http://www.nature.com/news/2010/100322/full/news.2010.140.html Nature News] [http://www.the-scientist.com/blog/display/57252/ The Scientist(blog)] [http://www.nytimes.com/2010/04/27/science/27gene.html NY Times] [http://genomebiology.com/2010/11/4/116 Genome Biology]
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<li value="110"> {{Paper
|title=Reducing MCM levels in human primary T cells during the G0->G1 transition causes genomic instability during the first cell cycle
|title=Revisiting the negative example sampling problem for predicting protein-protein interactions
|authors=Orr SJ, Gaymes T, Ladon D, Chronis C, Czepulkowski B, Wang R, Mufti GJ, Marcotte EM, Thomas NSB
|authors=Park Y, Marcotte EM
|journal=Oncogene
|journal=Bioinformatics
|pub_year=2010
|pubmed=21908540
|volume=29(26)
|page=3024-3028
|page=3803-14
|pub_year=2011
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|volume=27(21)
|pdf=Oncogene_MCM_2010.pdf
|pdf=Bioinformatics_NegativePPISampling_2011.pdf
|pubmed=20440261
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<li value="109"> {{Paper
|title=Rational association of genes with traits using a genome-scale gene network for <i>Arabidopsis thaliana</i>
|title=Systematic prediction of gene function using a probabilistic functional gene network for <i>Arabidopsis thaliana</i>
|authors=Lee I, Ambaru B, Thakkar P, Marcotte EM, Rhee SY
|authors=Hwang S, Rhee SY, Marcotte EM, Lee I
|journal=Nature Biotechnology
|journal=Nature Protocols
|pub_year=2010
|pubmed=21886106
|volume=28(2)
|pub_year=2011
|page=149-156
|volume=6
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|pdf=NatureProtocols_AraNet_2011.pdf
|link=https://www.nature.com/articles/nbt.1603
|page=1429–1442
|pdf=NatureBiotech_AraNet_2010.pdf
|link=http://dx.doi.org/10.1038/nprot.2011.372
|comment=[http://www.marcottelab.org/paper-pdfs/NatureBiotech_AraNet_2010_supplement.pdf Supplement] [http://www.marcottelab.org/paper-pdfs/848.full.pdf Honorable Mention in the 2010 Science Visualization Challenge] [http://www.nytimes.com/slideshow/2011/02/17/science/20110217-visualize-6.html New York Times slideshow ]
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<li value="108"> {{Paper
 
|title=Prioritizing candidate disease genes by network-based boosting of genome-wide association data
== 2009 ==
|authors=Lee I, Blom M, Wang PI, Shim JE, Marcotte EM
<ol>
|journal=Genome Research
 
|pubmed=21536720
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|pub_year=2011
|title=Rational extension of the ribosome biogenesis pathway using network-guided genetics
|volume=21(7)
|authors=Li Z, Lee I, Moradi E, Hung NJ, White J, Johnson AW, Marcotte EM
|pdf=GenomeResearch_HumanNet_2011.pdf
|journal=PLoS Biology
|page=1109-21
|pub_year=2009
|link=http://dx.doi.org/10.1101/gr.118992.110
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|title=Human cell chips: adapting DNA microarray spotting technology to cell-based imaging assays
|title=MSblender: a probabilistic approach for integrating peptide identifications from multiple database search engines
|authors=Hart GT, Zhao A, Garg A, Bolusani S, Marcotte EM
|authors=Kwon T, Choi H, Vogel C, Nesvizhskii AI, Marcotte EM
|journal=PLoS One
|journal=Journal of Proteome Research
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|pubmed=21488652
|volume=4(10)
|pub_year=2011
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|volume=10(7)
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|link=http://dx.doi.org/10.1371/journal.pone.0007088
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|pdf=PLoSOne_HumanCellChips_2009.pdf
|link=http://pubs.acs.org/doi/abs/10.1021/pr2002116
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|title=Ribosome stalk assembly requires the dual specificity phosphatase Yvh1 for the exchange of Mrt4 with P0
|title=A two-tiered approach identifies a network of cancer and liver diseases related genes regulated by miR-122
|authors=Lo KY, Li Z, Wang F, Marcotte EM, Johnson AF
|authors=Boutz DR, Collins P, Suresh U, Lu M, Ramírez CM, Fernández-Hernando C, Huang Y, de Sousa Abreu R, Le SY, Shapiro BA, Liu AM, Luk JM, Aldred SF, Trinklein N, Marcotte EM, Penalva LO
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|pdf=JBC_miR-122_2011.pdf
|link=http://dx.doi.org/10.1083/jcb.200904110
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<li value="90"> {{Paper
<li value="105"> {{Paper
|title=Absolute abundance for the masses
|title=High-throughput immunofluorescence microscopy using yeast spheroplast microarrays
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|journal=Nature Biotechnology
|journal=Methods in Molecular Biology: Cell-Based Microarrays
|pub_year=2009
|pub_year=2011
|volume=27(9)
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<li value="104"> {{Paper
|title=Global signatures of protein and mRNA expression levels
|title=A role for central spindle proteins in cilia structure and function
|authors=de Sousa Abreu R, Penalva LO, Marcotte EM, Vogel C
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|journal=Molecular BioSystems
|journal=Cytoskeleton
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|volume=5
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|authors=Gray RS, Abitua PB, Wlodarczyk BJ, Blanchard O, Lee I, Weiss G, Marcotte EM, Wallingford JB, Finnell RH
== 2010 ==
|journal=Nature Cell Biology
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|page=1225-32
|title=Parallel evolution in <i>Pseudomonas aeruginosa</i> over 39,000 generations <i>in vivo</i>
|pubmed=19767740
|authors=Huse HK, Kwon T, Zlosnik JEA, Speert DP, Marcotte EM, Whiteley M
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|pub_year=2010
|pdf=NatureCellBiology_Fuzzy_2009.pdf
|volume=1(4)
|pubmed=20856824
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|link=http://mbio.asm.org/content/1/4/e00199-10
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|pubmed=19563759
|page=article 400
|link=http://dx.doi.org/doi:10.1016/j.cell.2009.04.048   
|pdf=MolecularSystemsBiology_2010_HumanProteomics.pdf
|comment=[http://www.marcottelab.org/paper-pdfs/Cell_EdgeDetector_2009_Supplement.pdf Supplemental methods]
|link=http://www.nature.com/msb/journal/v6/n1/full/msb201059.html
|pdf=Cell_EdgeDetector_2009.pdf  
|comment=[http://www.marcottelab.org/paper-pdfs/MolecularSystemsBiology_2010_HumanProteomics_Supplement.pdf Supplement] [http://www.marcottelab.org/paper-pdfs/MolecularSystemsBiology_2010_HumanProteomics_S1.xls Supplemental Data (Excel format)] [http://www.marcottelab.org/paper-pdfs/MolecularSystemsBiology_2010_HumanProteomics_Fig2SourceData.txt Fig 2 source data] [http://www.marcottelab.org/paper-pdfs/MolecularSystemsBiology_2010_HumanProteomics_Fig2SourceData.txt Fig 3A source data] [http://www.marcottelab.org/paper-pdfs/MolecularSystemsBiology_2010_HumanProteomics_Fig2SourceData.txt Fig 3B source data] [http://www.marcottelab.org/paper-pdfs/MolecularSystemsBiology_2010_HumanProteomics_NewsAndViews.pdf News and Views]
}}
}}
</li>
</li>
<li value="83"> {{Paper
<li value="98"> {{Paper
|title=Effects of functional bias on supervised learning of a gene network model
|title=Defining the pathway of cytoplasmic maturation of the 60S ribosomal subunit
|authors=Lee I, Marcotte EM
|authors=Lo K-Y, Li Z, Bussiere C, Bresson S, Marcotte EM, Johnson AW
|journal=Methods Mol Biol
|journal=Molecular Cell
|pub_year=2009
|pub_year=2010
|volume=541
|volume=39(2)
|page=463-75
|page=196-208
|pubmed=19381535
|pubmed=20670889
|link=http://www.springerlink.com/content/j1726u1h54440624/
|pdf=MolecularCell_60SBiogenesis_2010.pdf
|comment=
|link=http://www.cell.com/molecular-cell/fulltext/S1097-2765(10)00459-4
|pdf=MethodsMolBioCompSysBio_Lee_2009_printersproofs.pdf
|comment=[http://www.marcottelab.org/paper-pdfs/MolecularCell_60SBiogenesis_2010_Supplement.pdf Supplement]
}}
}}
</li>
</li>
<li value="82"> {{Paper
<li value="97"> {{Paper
|title=Integrating shotgun proteomics and mRNA expression data to improve protein identification
|title=Predicting genetic modifier loci using functional gene networks
|authors=Ramakrishnan SR, Vogel C, Prince JT, Wang R, Li Z, Penalva LO, Myers M, Marcotte EM, Miranker DP
|authors=Lee I, Lehner B, Vavouri T, Shin J, Fraser AG, Marcotte EM
|journal=Bioinformatics
|journal=Genome Research
|pub_year=2009
|pub_year=2010
|volume=25(11)
|volume=20
|page=1397-403
|page=1143-1153
|pubmed=19318424
|pubmed=20538624
|link=http://bioinformatics.oxfordjournals.org/cgi/content/full/25/11/1397
|pdf=GenomeResearch_GeneticModifiers_2010.pdf
|comment=[http://www.marcottelab.org/paper-pdfs/Bioinformatics_mspresso_2009_Supplement.pdf Supplement] [http://www.marcottelab.org/MSpresso/ Supplemental website]
|link=http://dx.doi.org/10.1101/gr.102749.109
|pdf=Bioinformatics_mspresso_2009.pdf
|comment=[http://www.marcottelab.org/paper-pdfs/GenomeResearch_GeneticModifiers_2010_SOM.pdf Supplement] [http://www.nature.com/nrg/journal/vaop/ncurrent/full/nrg2836.html Nature Reviews Genetics]
}}
}}
</li>
</li>
<li value="81"> {{Paper
<li value="96"> {{Paper
|title=Systematic definition of protein constituents along the major polarization axis reveals an adaptive reuse of the polarization machinery in pheromone-treated budding yeast.
|title=Systematic discovery of nonobvious human disease models through orthologous phenotypes
|authors=Narayanaswamy R, Moradi EK, Niu W, Hart GT, Davis M, McGary KL, Ellington AD, Marcotte EM.
|authors=McGary KL, Park TJ, Woods JO, Cha HJ, Wallingford JB, Marcotte EM
|journal=J Proteome Res.
|journal=Proc Natl Acad Sci U S A
|pub_year=2009
|pub_year=2010
|volume=8(1)
|volume=107(14)
|page=6-19.
|page=6544-9
|pubmed=19053807
|pubmed=20308572
|link=http://pubs.acs.org/doi/abs/10.1021/pr800524g
|link=http://www.pnas.org/cgi/doi/10.1073/pnas.0910200107
|comment=
|pdf=PNAS_Phenologs_2010.pdf
|pdf=JProteomeResearch_Shmoo_2008.pdf
|comment=[http://www.marcottelab.org/paper-pdfs/PNAS_Phenologs_2010_Supplement.pdf Supplement] [http://www.nature.com/news/2010/100322/full/news.2010.140.html Nature News] [http://www.the-scientist.com/blog/display/57252/ The Scientist(blog)] [http://www.nytimes.com/2010/04/27/science/27gene.html NY Times] [http://genomebiology.com/2010/11/4/116 Genome Biology]
}}
</li>
<li value="95"> {{Paper
|title=Reducing MCM levels in human primary T cells during the G0->G1 transition causes genomic instability during the first cell cycle
|authors=Orr SJ, Gaymes T, Ladon D, Chronis C, Czepulkowski B, Wang R, Mufti GJ, Marcotte EM, Thomas NSB
|journal=Oncogene
|pub_year=2010
|volume=29(26)
|page=3803-14
|link=http://www.nature.com/onc/journal/vaop/ncurrent/abs/onc2010138a.html
|pdf=Oncogene_MCM_2010.pdf
|pubmed=20440261
}}
</li>
<li value="94"> {{Paper
|title=Rational association of genes with traits using a genome-scale gene network for <i>Arabidopsis thaliana</i>
|authors=Lee I, Ambaru B, Thakkar P, Marcotte EM, Rhee SY
|journal=Nature Biotechnology
|pub_year=2010
|volume=28(2)
|page=149-156
|pubmed=20118918
|link=https://www.nature.com/articles/nbt.1603
|pdf=NatureBiotech_AraNet_2010.pdf
|comment=[http://www.marcottelab.org/paper-pdfs/NatureBiotech_AraNet_2010_supplement.pdf Supplement] [http://www.marcottelab.org/paper-pdfs/848.full.pdf Honorable Mention in the 2010 Science Visualization Challenge] [http://www.nytimes.com/slideshow/2011/02/17/science/20110217-visualize-6.html New York Times slideshow ]
}}
}}
</li>
</li>
</ol>
</ol>


== 2008 ==
== 2009 ==
<ol>
<ol>
<li value="80"> {{Paper
 
|authors=Hannay K, Marcotte EM, Vogel C
<li value="93"> {{Paper
|title=Buffering by gene duplicates: an analysis of molecular correlates and evolutionary conservation
|title=Rational extension of the ribosome biogenesis pathway using network-guided genetics
|journal=BMC Genomics
|authors=Li Z, Lee I, Moradi E, Hung NJ, White J, Johnson AW, Marcotte EM
|pub_year=2008
|journal=PLoS Biology
|volume=9
|pub_year=2009
|page=609
|volume=7(10)
|pubmed=19087332
|page=e1000213
|link=http://www.biomedcentral.com/1471-2164/9/609
|pubmed=19806183
|pdf=BMCGenomics_Buffering_2008.pdf
|link=http://dx.doi.org/10.1371/journal.pbio.1000213
|comment=[http://www.marcottelab.org/paper-pdfs/BMCGenomics_Buffering_2008_SupplementalNotes.pdf Supplemental Notes] [http://www.marcottelab.org/paper-pdfs/BMCGenomics_Buffering_2008_SupplementalData.xls Supplemental Data]
|pdf=PLoSBiology_RibosomeBiogenesis_2009.pdf
|comment=[http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1000213#s5 Supplemental Figures and Tables]
}}
}}
</li>
</li>
<li value="79"> {{Paper
<li value="92"> {{Paper
|title=The APEX Quantitative Proteomics Tool: generating protein quantitation estimates from LC-MS/MS proteomics results
|title=Human cell chips: adapting DNA microarray spotting technology to cell-based imaging assays
|authors=Braisted JC, Kuntumalla S, Vogel C, Marcotte EM, Rodrigues AR, Wang R, Huang ST, Ferlanti ES, Saeed AI, Fleischmann RD, Peterson SN, Pieper R
|authors=Hart GT, Zhao A, Garg A, Bolusani S, Marcotte EM
|journal=BMC Bioinformatics
|journal=PLoS One
|pub_year=2008
|pub_year=2009
|volume=9
|volume=4(10)
|page=529.
|page=e7088
|pubmed=19068132
|pubmed=19862318
|link=http://www.biomedcentral.com/1471-2105/9/529
|link=http://dx.doi.org/10.1371/journal.pone.0007088
|pdf=BMCBioinformatics_APEXTool_2009.pdf
|pdf=PLoSOne_HumanCellChips_2009.pdf
|comment=
|comment=[http://www.marcottelab.org/paper-pdfs/PLoSOne_HumanCellChips_2009_TableS1.xls Table S1]
}}
}}
</li>
</li>
<li value="78"> {{Paper
<li value="91"> {{Paper
|title=Age-dependent evolution of the yeast protein interaction network suggests a limited role of gene duplication and divergence
|title=Ribosome stalk assembly requires the dual specificity phosphatase Yvh1 for the exchange of Mrt4 with P0
|authors=Kim WK, Marcotte EM
|authors=Lo KY, Li Z, Wang F, Marcotte EM, Johnson AF
|journal=PLoS Comput Biol
|journal=J. Cell Biology
|pub_year=2008
|pub_year=2009
|volume=4(11)
|volume=186(6)
|page=e1000232
|page=849-62
|pubmed=19043579
|pubmed=19797078
|link=http://dx.doi.org/10.1371/journal.pcbi.1000232
|link=http://dx.doi.org/10.1083/jcb.200904110
|pdf=PLoSComputationalBiology_PPINetworkEvolution_2008.pdf
|comment=[http://www.marcottelab.org/paper-pdfs/JCellBiol_Yvh1_2009_Supplement.pdf Supplemental material]
|comment=Supporting python code: [http://www.marcottelab.org/paper-pdfs/network_growth_functions_fixed_module.py network_growth_functions_fixed_module.py] Note that this code used an older version of the igraph library (0.4.2); the latest version that we've tested (0.5.2) gives somewhat fewer large clusters than our published clusters due to changes in the function "G.community_fastgreedy()", possibly resulting from modifications to the handling of ties in the community merging process. The previous igraph library (0.4.2) is linked here: [http://www.marcottelab.org/paper-pdfs/python-igraph-0.4.2.tar.gz python-igraph-0.4.2.tar.gz] [http://www.marcottelab.org/paper-pdfs/igraph-0.4.2.tar.gz igraph-0.4.2.tar.gz] [http://www.marcottelab.org/paper-pdfs/igraph_base.py igraph_base.py]
||pdf=JCellBiol_Yvh1_2009.pdf
}}
}}
</li>
</li>
<li value="77"> {{Paper
<li value="90"> {{Paper
|title=mspire: mass spectrometry proteomics in Ruby
|title=Absolute abundance for the masses
|authors=Prince JT, Marcotte EM
|authors=Vogel C, Marcotte EM
|journal=Bioinformatics
|journal=Nature Biotechnology
|pub_year=2008
|pub_year=2009
|volume=24(23)
|volume=27(9)
|page=2796-7
|page=825-6
|pubmed=18930952
|pubmed=19741640
|link=http://bioinformatics.oxfordjournals.org/cgi/content/full/24/23/2796
|link=http://dx.doi.org/10.1038/nbt0909-825
|pdf=Bioinformatics_mspire_2008.pdf
|pdf=NatureBiotech_MSNewsAndViews_2009.pdf
|comment=
|comment=
}}
}}
</li>
</li>
<li value="76"> {{Paper
<li value="89"> {{Paper
|title=Calculating absolute and relative protein abundance from mass spectrometry-based protein expression data
|title=Global signatures of protein and mRNA expression levels
|authors=Vogel C, Marcotte EM
|authors=de Sousa Abreu R, Penalva LO, Marcotte EM, Vogel C
|journal=Nat Protoc
|journal=Molecular BioSystems
|pub_year=2008
|pub_year=2009
|volume=3(9)
|volume=5
|page=1444-51.
|page=1512–1526
|pubmed=18772871
|pubmed=20023718
|link=http://www.nature.com/nprot/journal/v3/n9/abs/nprot.2008.132.html
|link=http://www.rsc.org/Publishing/Journals/MB/article.asp?doi=b908315d
|pdf=NatureProtocols_APEX_2008.pdf
|pdf=MolecularBioSystems_ProteinRNA_2009.pdf
|comment=[http://www.marcottelab.org/paper-pdfs/NatureProtocols_APEX_2008_Supplement.pdf Supplement]
|comment=
}}
}}
</li>
</li>
<li value="75"> {{Paper
<li value="88"> {{Paper
|title=Integrating functional genomics data
|title=The planar cell polarity effector protein Fuzzy is essential for targeted membrane trafficking, ciliogenesis, and mouse embryonic development
|authors=Lee I, Marcotte EM
|authors=Gray RS, Abitua PB, Wlodarczyk BJ, Blanchard O, Lee I, Weiss G, Marcotte EM, Wallingford JB, Finnell RH
|journal=Methods Mol Biol
|journal=Nature Cell Biology
|pub_year=2008
|pub_year=2009
|volume=453
|volume=11(10)
|page=267-78.
|page=1225-32
|pubmed=18712309
|pubmed=19767740
|link=http://www.springerlink.com/content/h21044190m77k274/
|link=http://dx.doi.org/10.1038/ncb1966
|pdf=MethodsMolBioBioinformatics_LeeMarcotte_2008.pdf
|comment=[http://www.nature.com/ncb/journal/v11/n10/covers/index.html Journal cover--a beautiful electron micrograph by Phil Abitua] [http://www.marcottelab.org/paper-pdfs/NatureCellBiology_Fuzzy_2009_supplement.pdf Supplemental Figures] [[File:NatureCellBiologyFuzCover2009.jpg||100px|right]]
|pdf=NatureCellBiology_Fuzzy_2009.pdf
}}
</li>
<li value="87"> {{Paper
|title=Disorder, promiscuity, and toxic partnerships
|authors=Marcotte EM, Tsechansky M
|journal=Cell
|pub_year=2009
|volume=138(1)
|page=16-18
|pubmed=19596229 
|link=http://dx.doi.org/10.1016/j.cell.2009.06.024   
|comment=
|comment=
|pdf=Cell_LehnerPreview_2009.pdf
}}
}}
</li>
</li>
<li value="74"> {{Paper
<li value="86"> {{Paper
|title=Inferring mouse gene functions from genomic-scale data using a combined functional network/classification strategy
|title=Mining gene functional networks to improve mass-spectrometry based protein identification
|authors=Kim WK, Krumpelman C, Marcotte EM
|authors=Ramakrishnan SR, Vogel C, Kwon T, Penalva LO, Marcotte EM, Miranker DP
|journal=Genome Biol
|journal=Bioinformatics
|pub_year=2008
|pub_year=2009
|volume=9 Suppl 1:
|volume=25(22)
|page=S5
|page=2955-2961
|pubmed=18613949
|pubmed=19633097
|link=http://genomebiology.com/2008/9/S1/S5
|link=http://bioinformatics.oxfordjournals.org/cgi/reprint/btp461
|pdf=GenomeBiology_MouseNet_2008.pdf
|pdf=Bioinformatics_MSNet_2009.pdf
|comment=[http://www.marcottelab.org/paper-pdfs/GenomeBiology_MouseNet_2008_Supplement.pdf Supplement]
|comment=[http://aug.csres.utexas.edu/msnet/ Supplemental Website]
}}
}}
</li>
</li>
<li value="73"> {{Paper
<li value="85"> {{Paper
|title=A critical assessment of <i>Mus musculus</i> gene function prediction using integrated genomic evidence
|title=Widespread reorganization of metabolic enzymes into reversible assemblies upon nutrient starvation
|authors=Peña-Castillo L, Tasan M, Myers CL, Lee H, Joshi T, Zhang C, Guan Y, Leone M, Pagnani A, Kim WK, Krumpelman C, Tian W, Obozinski G, Qi Y, Mostafavi S, Lin GN, Berriz GF, Gibbons FD, Lanckriet G, Qiu J, Grant C, Barutcuoglu Z, Hill DP, Warde-Farley D, Grouios C, Ray D, Blake JA, Deng M, Jordan MI, Noble WS, Morris Q, Klein-Seetharaman J, Bar-Joseph Z, Chen T, Sun F, Troyanskaya OG, Marcotte EM, Xu D, Hughes TR, Roth FP
|authors=Narayanaswamy R, Levy M, Tsechansky M, Stovall GM, O'Connell J, Mirrielees J, Ellington AD, Marcotte EM
|journal=Genome Biol
|journal=Proc Natl Acad Sci U S A
|pub_year=2008
|pub_year=2009
|volume=9 Suppl 1
|volume=106(25)
|page=S2
|page=10147-52
|pubmed=18613946
|pubmed=19502427
|link=http://genomebiology.com/2008/9/S1/S2
|link=http://www.pnas.org/content/106/25/10147.long
|pdf=GenomeBiology_MouseFunc_2008.pdf
|comment=[http://www.marcottelab.org/paper-pdfs/PNAS_punctatebodies_2009_Supplement.pdf Supplemental methods] [http://www.marcottelab.org/paper-pdfs/PNAS_punctatebodies_2009_SupplementalDataset.xls Supplemental Dataset] [http://www.marcottelab.org/paper-pdfs/PNAS_punctatebodies_2009_TableS1.pdf Table S1] [http://www.marcottelab.org/paper-pdfs/PNAS_punctatebodies_2009_TableS2.pdf Table S2] [http://www.marcottelab.org/paper-pdfs/PNAS_punctatebodies_2009_TableS3.pdf Table S3]
|comment=[http://func.med.harvard.edu/ MouseFunc predictions]
|pdf=PNAS_punctatebodies_2009.pdf
}}
}}
</li>
</li>
<li value="72"> {{Paper
<li value="84"> {{Paper
|title=Mechanisms of cell cycle control revealed by a systematic and quantitative overexpression screen in <i>S. cerevisiae</i>
|title=A synthetic genetic edge detection program
|authors=Niu W, Li Z, Zhan W, Iyer VR, Marcotte EM
|authors=Tabor JJ, Salis H, Simpson ZB, Chevalier AA, Levskaya A, Marcotte EM, Voigt CA, Ellington AD
|journal=PLoS Genet
|journal=Cell
|pub_year=2008
|pub_year=2009
|volume=4(7)
|volume=137(7)
|page=e1000120
|page=1272-1281
|pubmed=18617996
|pubmed=19563759
|link=http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000120
|link=http://dx.doi.org/doi:10.1016/j.cell.2009.04.048   
|pdf=PLoSGenetics_CellCycleScreen_2008.pdf
|comment=[http://www.marcottelab.org/paper-pdfs/Cell_EdgeDetector_2009_Supplement.pdf Supplemental methods]
|comment=[http://www.marcottelab.org/paper-pdfs/Niu_et_al_MORF_strains_cell_cnt_gt5000_Z_scores.xls Supplemental File of All ORF FACS Defects]  
|pdf=Cell_EdgeDetector_2009.pdf
}}
}}
</li>
</li>
<li value="71"> {{Paper
<li value="83"> {{Paper
|title=Group II intron protein localization and insertion sites are affected by polyphosphate
|title=Effects of functional bias on supervised learning of a gene network model
|authors=Zhao J, Niu W, Yao J, Mohr S, Marcotte EM, Lambowitz AM
|authors=Lee I, Marcotte EM
|journal=PLoS Biol
|journal=Methods Mol Biol
|pub_year=2008
|pub_year=2009
|volume=6(6)
|volume=541
|page=e150
|page=463-75
|pubmed=18593213
|pubmed=19381535
|link=http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.0060150
|link=http://www.springerlink.com/content/j1726u1h54440624/
|pdf=PLoSBiology_IntronLocalization_2008.pdf
|comment=
|comment=
|pdf=MethodsMolBioCompSysBio_Lee_2009_printersproofs.pdf
}}
}}
</li>
</li>
<li value="70"> {{Paper
<li value="82"> {{Paper
|title=A map of human protein interactions derived from co-expression of human mRNAs and their orthologs
|title=Integrating shotgun proteomics and mRNA expression data to improve protein identification
|authors=Ramani AK, Li Z, Hart GT, Carlson MW, Boutz DR, Marcotte EM
|authors=Ramakrishnan SR, Vogel C, Prince JT, Wang R, Li Z, Penalva LO, Myers M, Marcotte EM, Miranker DP
|journal=Mol Syst Biol
|journal=Bioinformatics
|pub_year=2008
|pub_year=2009
|volume=4
|volume=25(11)
|page=180
|page=1397-403
|pubmed=18414481
|pubmed=19318424
|link=http://dx.doi.org/10.1038/msb.2008.19
|link=http://bioinformatics.oxfordjournals.org/cgi/content/full/25/11/1397
|pdf=MolSysBiol_CCE_2008.pdf
|comment=[http://www.marcottelab.org/paper-pdfs/Bioinformatics_mspresso_2009_Supplement.pdf Supplement] [http://www.marcottelab.org/MSpresso/ Supplemental website]
|comment=
|pdf=Bioinformatics_mspresso_2009.pdf
}}
}}
</li>
</li>
<li value="69"> {{Paper
<li value="81"> {{Paper
|title=Bud23 methylates G1575 of 18S rRNA and is required for efficient nuclear export of pre-40S subunits
|title=Systematic definition of protein constituents along the major polarization axis reveals an adaptive reuse of the polarization machinery in pheromone-treated budding yeast.
|authors=White J, Li Z, Sardana R, Bujnicki JM, Marcotte EM, Johnson AW
|authors=Narayanaswamy R, Moradi EK, Niu W, Hart GT, Davis M, McGary KL, Ellington AD, Marcotte EM.
|journal=Mol Cell Biol
|journal=J Proteome Res.
|pub_year=2008
|pub_year=2009
|volume=28(10)
|volume=8(1)
|page=3151-61
|page=6-19.
|pubmed=18332120
|pubmed=19053807
|link=http://mcb.asm.org/cgi/content/full/28/10/3151
|link=http://pubs.acs.org/doi/abs/10.1021/pr800524g
|pdf=MolCellBiol_Bud23_2008.pdf
|comment=
|comment=
|pdf=JProteomeResearch_Shmoo_2008.pdf
}}
}}
</li>
</li>
<li value="68"> {{Paper
</ol>
|title=The proteomic response of <i>Mycobacterium smegmatis</i> to anti-tuberculosis drugs suggests targeted pathways
 
|authors=Wang R, Marcotte EM
== 2008 ==
|journal=J Proteome Res
<ol>
<li value="80"> {{Paper
|authors=Hannay K, Marcotte EM, Vogel C
|title=Buffering by gene duplicates: an analysis of molecular correlates and evolutionary conservation
|journal=BMC Genomics
|pub_year=2008
|pub_year=2008
|volume=7(3)
|volume=9
|page=855-65
|page=609
|pubmed=18275136
|pubmed=19087332
|link=http://pubs.acs.org/doi/abs/10.1021/pr0703066
|link=http://www.biomedcentral.com/1471-2164/9/609
|pdf=JProteomeResearch_TBDrug_2008.pdf
|pdf=BMCGenomics_Buffering_2008.pdf
|comment=
|comment=[http://www.marcottelab.org/paper-pdfs/BMCGenomics_Buffering_2008_SupplementalNotes.pdf Supplemental Notes] [http://www.marcottelab.org/paper-pdfs/BMCGenomics_Buffering_2008_SupplementalData.xls Supplemental Data]
}}
}}
</li>
</li>
<li value="67"> {{Paper
<li value="79"> {{Paper
|title=A single gene network accurately predicts phenotypic effects of gene perturbation in <i>Caenorhabditis elegans</i>
|title=The APEX Quantitative Proteomics Tool: generating protein quantitation estimates from LC-MS/MS proteomics results
|authors=Lee I, Lehner B, Crombie C, Wong W, Fraser AG, Marcotte EM
|authors=Braisted JC, Kuntumalla S, Vogel C, Marcotte EM, Rodrigues AR, Wang R, Huang ST, Ferlanti ES, Saeed AI, Fleischmann RD, Peterson SN, Pieper R
|journal=Nat Genet
|journal=BMC Bioinformatics
|pub_year=2008
|pub_year=2008
|volume=40(2)
|volume=9
|page=181-8
|page=529.
|pubmed=18223650
|pubmed=19068132
|link=http://www.nature.com/ng/journal/v40/n2/abs/ng.2007.70.html
|link=http://www.biomedcentral.com/1471-2105/9/529
|pdf=NatureGenetics_Wormnet_2008.pdf
|pdf=BMCBioinformatics_APEXTool_2009.pdf
|comment=[http://www.marcottelab.org/paper-pdfs/NatureGenetics_Wormnet_2008_Supplement.pdf Supplement] [http://www.functionalnet.org/wormnet Supplemental Web Site] [[File:NatureGeneticsWormNetCover2008.jpg||100px|right]]
|comment=
 
}}
}}
</li>
</li>
</ol>
<li value="78"> {{Paper
 
|title=Age-dependent evolution of the yeast protein interaction network suggests a limited role of gene duplication and divergence
== 2007 ==
|authors=Kim WK, Marcotte EM
<ol>
|journal=PLoS Comput Biol
<li value="66"> {{Paper
|pub_year=2008
|title=Broad network-based predictability of <i>Saccharomyces cerevisiae</i> gene loss-of-function phenotypes
|volume=4(11)
|authors=McGary KL, Lee I, Marcotte EM
|page=e1000232
|journal=Genome Biol
|pubmed=19043579
|pub_year=2007
|link=http://dx.doi.org/10.1371/journal.pcbi.1000232
|volume=8(12)
|pdf=PLoSComputationalBiology_PPINetworkEvolution_2008.pdf
|page=R258.
|comment=Supporting python code: [http://www.marcottelab.org/paper-pdfs/network_growth_functions_fixed_module.py network_growth_functions_fixed_module.py] Note that this code used an older version of the igraph library (0.4.2); the latest version that we've tested (0.5.2) gives somewhat fewer large clusters than our published clusters due to changes in the function "G.community_fastgreedy()", possibly resulting from modifications to the handling of ties in the community merging process. The previous igraph library (0.4.2) is linked here: [http://www.marcottelab.org/paper-pdfs/python-igraph-0.4.2.tar.gz python-igraph-0.4.2.tar.gz] [http://www.marcottelab.org/paper-pdfs/igraph-0.4.2.tar.gz igraph-0.4.2.tar.gz] [http://www.marcottelab.org/paper-pdfs/igraph_base.py igraph_base.py]
|pubmed=18053250
|link=http://genomebiology.com/2007/8/12/R258
|pdf=GenomeBiology_YeastPhenoPred_2007.pdf
|comment=[http://www.yeastnet.org Supplemental Web Site]
}}
}}
</li>
</li>
<li value="65"> {{Paper
<li value="77"> {{Paper
|title=An improved, bias-reduced probabilistic functional gene network of baker's yeast, <i>Saccharomyces cerevisiae</i>
|title=mspire: mass spectrometry proteomics in Ruby
|authors=Lee I, Li Z, Marcotte EM
|authors=Prince JT, Marcotte EM
|journal=PLoS ONE
|journal=Bioinformatics
|pub_year=2007
|pub_year=2008
|volume=2(10)
|volume=24(23)
|page=e988
|page=2796-7
|pubmed=17912365
|pubmed=18930952
|link=http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0000988
|link=http://bioinformatics.oxfordjournals.org/cgi/content/full/24/23/2796
|pdf=PLOS1_YeastNet2_2007.pdf
|pdf=Bioinformatics_mspire_2008.pdf
|comment=[http://www.yeastnet.org Supplemental Web Site]
|comment=
}}
}}
</li>
</li>
<li value="64"> {{Paper
<li value="76"> {{Paper
|title=How do shotgun proteomics algorithms identify proteins?
|title=Calculating absolute and relative protein abundance from mass spectrometry-based protein expression data
|authors=Marcotte EM
|authors=Vogel C, Marcotte EM
|journal=Nat Biotechnol
|journal=Nat Protoc
|pub_year=2007
|pub_year=2008
|volume=25(7)
|volume=3(9)
|page=755-7
|page=1444-51.
|pubmed=17621303
|pubmed=18772871
|link=http://www.nature.com/nbt/journal/v25/n7/abs/nbt0707-755.html
|link=http://www.nature.com/nprot/journal/v3/n9/abs/nprot.2008.132.html
|pdf=NatureBiotech_ShotgunProteomicsPrimer_2007.pdf
|pdf=NatureProtocols_APEX_2008.pdf
|comment=
|comment=[http://www.marcottelab.org/paper-pdfs/NatureProtocols_APEX_2008_Supplement.pdf Supplement]
}}
}}
</li>
</li>
<li value="63"> {{Paper
<li value="75"> {{Paper
|title=Quantitative gene expression assessment identifies appropriate cell line models for individual cervical cancer pathways
|title=Integrating functional genomics data
|authors=Carlson MW, Iyer VR, Marcotte EM
|authors=Lee I, Marcotte EM
|journal=BMC Genomics
|journal=Methods Mol Biol
|pub_year=2007
|pub_year=2008
|volume=8
|volume=453
|page=117.
|page=267-78.
|pubmed=17493265
|pubmed=18712309
|link=http://www.biomedcentral.com/1471-2164/8/117
|link=http://www.springerlink.com/content/h21044190m77k274/
|pdf=BMCGenomics_CervicalCancer_2007.pdf
|pdf=MethodsMolBioBioinformatics_LeeMarcotte_2008.pdf
|comment=
|comment=
}}
}}
</li>
</li>
<li value="62"> {{Paper
<li value="74"> {{Paper
|title=Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation
|title=Inferring mouse gene functions from genomic-scale data using a combined functional network/classification strategy
|authors=Lu P, Vogel C, Wang R, Yao X, Marcotte EM
|authors=Kim WK, Krumpelman C, Marcotte EM
|journal=Nat Biotechnol
|journal=Genome Biol
|pub_year=2007
|pub_year=2008
|volume=25(1)
|volume=9 Suppl 1:
|page=117-24
|page=S5
|pubmed=17187058
|pubmed=18613949
|link=http://www.nature.com/nbt/journal/v25/n1/abs/nbt1270.html
|link=http://genomebiology.com/2008/9/S1/S5
|pdf=NatureBiotech_APEX_2007.pdf
|pdf=GenomeBiology_MouseNet_2008.pdf
|comment=[http://www.marcottelab.org/paper-pdfs/NatureBiotech_APEX_2007_supplement.pdf Supplement] [http://www.marcottelab.org/paper-pdfs/NatureBiotech_APEX_2007_SupplementaryData.zip Supplemental Data (zipped folder)] [http://www.marcottelab.org/paper-pdfs/NatureBiotech_APEX_2007_newsandviews.pdf News & Views 1] [http://www.marcottelab.org/paper-pdfs/NatureBiotech_APEX_2007_newsandviews2.pdf News & Views 2] [http://www.marcottelab.org/paper-pdfs/NatureBiotech_APEX_2007_newsandviews3.pdf News & Views 3] [http://www.marcottelab.org/paper-pdfs/NatureBiotech_APEX_NBTretrospective_2011.pdf 2011 NBT Retrospective on APEX]
|comment=[http://www.marcottelab.org/paper-pdfs/GenomeBiology_MouseNet_2008_Supplement.pdf Supplement]
}}
}}
</li>
</li>
<li value="61"> {{Paper
<li value="73"> {{Paper
|title=Global metabolic changes following loss of a feedback loop reveal dynamic steady states of the yeast metabolome
|title=A critical assessment of <i>Mus musculus</i> gene function prediction using integrated genomic evidence
|authors=Lu P, Rangan A, Chan SY, Appling DR, Hoffman DW, Marcotte EM
|authors=Peña-Castillo L, Tasan M, Myers CL, Lee H, Joshi T, Zhang C, Guan Y, Leone M, Pagnani A, Kim WK, Krumpelman C, Tian W, Obozinski G, Qi Y, Mostafavi S, Lin GN, Berriz GF, Gibbons FD, Lanckriet G, Qiu J, Grant C, Barutcuoglu Z, Hill DP, Warde-Farley D, Grouios C, Ray D, Blake JA, Deng M, Jordan MI, Noble WS, Morris Q, Klein-Seetharaman J, Bar-Joseph Z, Chen T, Sun F, Troyanskaya OG, Marcotte EM, Xu D, Hughes TR, Roth FP
|journal=Metab Eng
|journal=Genome Biol
|pub_year=2007
|pub_year=2008
|volume=9(1)
|volume=9 Suppl 1
|page=8-20
|page=S2
|pubmed=17049899
|pubmed=18613946
|link=http://dx.doi.org/10.1016/j.ymben.2006.06.003
|link=http://genomebiology.com/2008/9/S1/S2
|pdf=MetabolicEngineering_OneCarbonMetab_2007.pdf
|pdf=GenomeBiology_MouseFunc_2008.pdf
|comment=[http://www.marcottelab.org/paper-pdfs/MetabolicEngineering_OneCarbonMetab_2007_SupplementalFile1.xls Supplemental File 1] [http://www.marcottelab.org/paper-pdfs/MetabolicEngineering_OneCarbonMetab_2007_SupplementalFile2.xls Supplemental File 2] [http://www.marcottelab.org/paper-pdfs/MetabolicEngineering_OneCarbonMetab_2007_SupplementalFile3.xls Supplemental File 3]
|comment=[http://func.med.harvard.edu/ MouseFunc predictions]
}}
}}
</li>
</li>
<li value="60"> {{Paper
<li value="72"> {{Paper
|title=A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality
|title=Mechanisms of cell cycle control revealed by a systematic and quantitative overexpression screen in <i>S. cerevisiae</i>
|authors=Hart GT, Lee I, Marcotte EM
|authors=Niu W, Li Z, Zhan W, Iyer VR, Marcotte EM
|journal=BMC Bioinformatics
|journal=PLoS Genet
|pub_year=2007
|pub_year=2008
|volume=8
|volume=4(7)
|page=236.
|page=e1000120
|pubmed=17605818
|pubmed=18617996
|link=http://www.biomedcentral.com/1471-2105/8/236
|link=http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000120
|pdf=BMCBioinformatics_YeastComplexEssentiality_2007.pdf
|pdf=PLoSGenetics_CellCycleScreen_2008.pdf
|comment=
|comment=[http://www.marcottelab.org/paper-pdfs/Niu_et_al_MORF_strains_cell_cnt_gt5000_Z_scores.xls Supplemental File of All ORF FACS Defects]
}}
}}
</li>
</li>
</ol>
<li value="71"> {{Paper
 
|title=Group II intron protein localization and insertion sites are affected by polyphosphate
== 2006 ==
|authors=Zhao J, Niu W, Yao J, Mohr S, Marcotte EM, Lambowitz AM
<ol>
|journal=PLoS Biol
<li value="59"> {{Paper
|pub_year=2008
|title=How complete are current yeast and human protein-interaction networks?
|volume=6(6)
|authors=Hart GT, Ramani AK, Marcotte EM.
|page=e150
|journal=Genome Biol.
|pubmed=18593213
|pub_year=2006
|link=http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.0060150
|volume=7(11)
|pdf=PLoSBiology_IntronLocalization_2008.pdf
|page=120
|comment=
|pubmed=17147767
|link=http://genomebiology.com/2006/7/11/120
|pdf=GenomeBiology_HumanPPIOverview_2006.pdf
|comment=[http://www.marcottelab.org/paper-pdfs/GenomeBiology_HumanPPIOverview_2006_AdditionalDataFile1.pdf Additional Data File 1]
}}
}}
</li>
</li>
<li value="58"> {{Paper
<li value="70"> {{Paper
|title=Chromatographic alignment of ESI-LC-MS proteomics datasets by ordered bijective interpolated warping
|title=A map of human protein interactions derived from co-expression of human mRNAs and their orthologs
|authors=Prince JT, Marcotte EM
|authors=Ramani AK, Li Z, Hart GT, Carlson MW, Boutz DR, Marcotte EM
|journal=Anal. Chem.
|journal=Mol Syst Biol
|pub_year=2006
|pub_year=2008
|volume=78(17)
|volume=4
|page=6140-52
|page=180
|pubmed=16944896
|pubmed=18414481
|link=http://pubs.acs.org/doi/abs/10.1021/ac0605344
|link=http://dx.doi.org/10.1038/msb.2008.19
|pdf=AnalyticalChemistry_OBIWarp_2006.pdf
|pdf=MolSysBiol_CCE_2008.pdf
|comment=
|comment=
}}
}}
</li>
</li>
<li value="57"> {{Paper
<li value="69"> {{Paper
|title=A fast coarse filtering method for peptide identification by mass spectrometry
|title=Bud23 methylates G1575 of 18S rRNA and is required for efficient nuclear export of pre-40S subunits
|authors=Ramakrishnan SR, Mao R, Nakorchevskiy AA, Prince JT, Willard WS, Xu W, Marcotte EM, Miranker DP
|authors=White J, Li Z, Sardana R, Bujnicki JM, Marcotte EM, Johnson AW
|journal=Bioinformatics
|journal=Mol Cell Biol
|pub_year=2006
|pub_year=2008
|volume=22(12)
|volume=28(10)
|page=1524-31
|page=3151-61
|pubmed=16585069
|pubmed=18332120
|link=http://bioinformatics.oxfordjournals.org/cgi/content/full/22/12/1524
|link=http://mcb.asm.org/cgi/content/full/28/10/3151
|pdf=Bioinformatics_MoBIoSCoarseFilter_2006.pdf
|pdf=MolCellBiol_Bud23_2008.pdf
|comment=
|comment=
}}
}}
</li>
</li>
<li value="56"> {{Paper
<li value="68"> {{Paper
|title=Systematic profiling of cellular phenotypes with spotted cell microarrays reveals new pheromone response genes
|title=The proteomic response of <i>Mycobacterium smegmatis</i> to anti-tuberculosis drugs suggests targeted pathways
|authors=Narayanaswamy R, Niu W, Scouras A, Hart GT, Davies J, Ellington AD, Iyer VR, Marcotte EM
|authors=Wang R, Marcotte EM
|journal=Genome Biol.
|journal=J Proteome Res
|pub_year=2006
|pub_year=2008
|volume=7(1)
|volume=7(3)
|page=R6
|page=855-65
|pubmed=16507139
|pubmed=18275136
|link=http://genomebiology.com/2006/7/1/R6
|link=http://pubs.acs.org/doi/abs/10.1021/pr0703066
|pdf=GenomeBiology_CellChips_2006.pdf
|pdf=JProteomeResearch_TBDrug_2008.pdf
|comment=[http://www.marcottelab.org/paper-pdfs/GenomeBiology_CellChips_Supplement_2006.pdf Supplement] [http://www.marcottelab.org/paper-pdfs/NarayanaswamySupplementalTable1.xls Supplemental Table 1] [http://www.marcottelab.org/paper-pdfs/NarayanaswamySupplementalTable2.xls Supplemental Table 2] [http://www.marcottelab.org/paper-pdfs/NarayanaswamySupplementalTable3.xls Supplemental Table 3] [http://www.marcottelab.org/paper-pdfs/NarayanaswamySupplementalTable4.xls Supplemental Table 4]
|comment=
}}
}}
</li>
</li>
<li value="55"> {{Paper
<li value="67"> {{Paper
|title=Bioinformatic prediction of yeast gene function
|title=A single gene network accurately predicts phenotypic effects of gene perturbation in <i>Caenorhabditis elegans</i>
|authors=Lee I, Narayanaswamy R, Marcotte EM
|authors=Lee I, Lehner B, Crombie C, Wong W, Fraser AG, Marcotte EM
|journal=Yeast Gene Analysis
|journal=Nat Genet
|pub_year=2006
|pub_year=2008
|volume=Stansfield, I., ed., Elsevier Press
|volume=40(2)
|page=
|page=181-8
|pubmed=
|pubmed=18223650
|link=
|link=http://www.nature.com/ng/journal/v40/n2/abs/ng.2007.70.html
|pdf=LeeNarayanaswamyMarcotteManuscript.pdf
|pdf=NatureGenetics_Wormnet_2008.pdf
|comment=
|comment=[http://www.marcottelab.org/paper-pdfs/NatureGenetics_Wormnet_2008_Supplement.pdf Supplement] [http://www.functionalnet.org/wormnet Supplemental Web Site] [[File:NatureGeneticsWormNetCover2008.jpg||100px|right]]
 
}}
}}
</li>
</li>
<li value="54"> {{Paper
</ol>
|title=Bioinformatic challenges for the next decade(s)
 
|authors=Eisenberg D, Marcotte E, McLachlan AD, Pellegrini M
== 2007 ==
|journal=Philos Trans R Soc Lond B Biol Sci.
<ol>
|pub_year=2006
<li value="66"> {{Paper
|volume=361(1467)
|title=Broad network-based predictability of <i>Saccharomyces cerevisiae</i> gene loss-of-function phenotypes
|page=525-7
|authors=McGary KL, Lee I, Marcotte EM
|pubmed=16524841
|journal=Genome Biol
|link=http://rstb.royalsocietypublishing.org/content/361/1467/525.long
|pub_year=2007
|pdf=PhilTransactionsRoyalSocB_BioinformaticChallenges_2006.pdf
|volume=8(12)
|comment=
|page=R258.
|pubmed=18053250
|link=http://genomebiology.com/2007/8/12/R258
|pdf=GenomeBiology_YeastPhenoPred_2007.pdf
|comment=[http://www.yeastnet.org Supplemental Web Site]
}}
}}
</li>
</li>
</ol>
<li value="65"> {{Paper
 
|title=An improved, bias-reduced probabilistic functional gene network of baker's yeast, <i>Saccharomyces cerevisiae</i>
== 2005 ==
|authors=Lee I, Li Z, Marcotte EM
<ol>
|journal=PLoS ONE
<li value="53"> {{Paper
|pub_year=2007
|title=Synthetic biology: Engineering ''Escherichia coli'' to see light
|volume=2(10)
|authors=Levskaya A, Chevalier AA, Tabor JJ, Simpson ZB, Lavery LA, Levy M, Davidson EA, Scouras A, Ellington AD, Marcotte EM, Voigt CA
|page=e988
|journal=Nature
|pubmed=17912365
|pub_year=2005
|link=http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0000988
|volume=438(7067)
|pdf=PLOS1_YeastNet2_2007.pdf
|page=441-2
|comment=[http://www.yeastnet.org Supplemental Web Site]
|pubmed=16306980 
|link=http://dx.doi.org/10.1038/nature04405
|pdf=Nature_BacterialPhotography_2005.pdf
|comment=[http://www.sciencedaily.com/releases/2005/11/051123171556.htm the Science Daily press release] [http://dx.doi.org/10.1038/4381064a <i>Nature</i> 2005 Gallery "First Glimpse"] [http://dx.doi.org/10.1038/438417a <i>Nature</i> feature on the iGEM competition featuring a bacterial portrait] [http://www.utexas.edu/features/2005/bacteria/ UT press release] [http://www.nytimes.com/2005/11/24/national/24film.html New York Times feature]
}}
}}
</li>
</li>
<li value="52"> {{Paper
<li value="64"> {{Paper
|title=A fast coarse filtering method for protein identification by mass spectrometry
|title=How do shotgun proteomics algorithms identify proteins?
|authors=Ramakrishnan SR, Mao R, Nakorchevskiy AA, Prince JT, Willard WS, Xu W, Marcotte EM, Miranker DP
|authors=Marcotte EM
|journal=University of Texas Dept. of Computer Sciences, Technical Report
|journal=Nat Biotechnol
|pub_year=2005
|pub_year=2007
|volume=TR-05-06
|volume=25(7)
|page=
|page=755-7
|pubmed=  
|pubmed=17621303
|link=
|link=http://www.nature.com/nbt/journal/v25/n7/abs/nbt0707-755.html
|pdf=TechnicalReport-MoBIoS-TR-05-06.pdf
|pdf=NatureBiotech_ShotgunProteomicsPrimer_2007.pdf
|comment=
|comment=
}}
}}
</li>
</li>
<li value="51"> {{Paper
<li value="63"> {{Paper
|title=Mass spectrometry of the <i>M. smegmatis</i> proteome: Protein expression levels correlate with function, operons, and codon bias
|title=Quantitative gene expression assessment identifies appropriate cell line models for individual cervical cancer pathways
|authors=Wang R, Prince JT, Marcotte EM
|authors=Carlson MW, Iyer VR, Marcotte EM
|journal=Genome Res.
|journal=BMC Genomics
|pub_year=2005
|pub_year=2007
|volume=15(8)
|volume=8
|page=1118-26
|page=117.
|pubmed=16077011
|pubmed=17493265
|link=http://genome.cshlp.org/content/15/8/1118.long
|link=http://www.biomedcentral.com/1471-2164/8/117
|pdf=rong_2005.pdf
|pdf=BMCGenomics_CervicalCancer_2007.pdf
|comment=
|comment=
}}
}}
</li>
</li>
<li value="50"> {{Paper
<li value="62"> {{Paper
|title=Consolidating the set of known human protein-protein interactions in preparation for large-scale mapping of the human interactome
|title=Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation
|authors=Ramani AK, Bunescu RC, Mooney RJ, Marcotte EM
|authors=Lu P, Vogel C, Wang R, Yao X, Marcotte EM
|journal=Genome Biology
|journal=Nat Biotechnol
|pub_year=2005
|pub_year=2007
|volume=6(5)
|volume=25(1)
|page=R40
|page=117-24
|pubmed=15892868 
|pubmed=17187058
|link=http://genomebiology.com/2005/6/5/R40
|link=http://www.nature.com/nbt/journal/v25/n1/abs/nbt1270.html
|pdf=Arun-consolidate-human.pdf
|pdf=NatureBiotech_APEX_2007.pdf
|comment=
|comment=[http://www.marcottelab.org/paper-pdfs/NatureBiotech_APEX_2007_supplement.pdf Supplement] [http://www.marcottelab.org/paper-pdfs/NatureBiotech_APEX_2007_SupplementaryData.zip Supplemental Data (zipped folder)] [http://www.marcottelab.org/paper-pdfs/NatureBiotech_APEX_2007_newsandviews.pdf News & Views 1] [http://www.marcottelab.org/paper-pdfs/NatureBiotech_APEX_2007_newsandviews2.pdf News & Views 2] [http://www.marcottelab.org/paper-pdfs/NatureBiotech_APEX_2007_newsandviews3.pdf News & Views 3] [http://www.marcottelab.org/paper-pdfs/NatureBiotech_APEX_NBTretrospective_2011.pdf 2011 NBT Retrospective on APEX]
}}
}}
</li>
</li>
<li value="49"> {{Paper
<li value="61"> {{Paper
|title=Comparative experiments on learning information extractors for proteins and their interactions
|title=Global metabolic changes following loss of a feedback loop reveal dynamic steady states of the yeast metabolome
|authors=Bunescu R, Ge R, Kate RJ, Marcotte EM, Mooney RJ, Ramani AK, Wong YW
|authors=Lu P, Rangan A, Chan SY, Appling DR, Hoffman DW, Marcotte EM
|journal=Artif Intell Med.
|journal=Metab Eng
|pub_year=2005
|pub_year=2007
|volume=33(2)
|volume=9(1)
|page=139-55
|page=8-20
|pubmed=15811782 
|pubmed=17049899
|link=http://dx.doi.org/10.1016/j.artmed.2004.07.016
|link=http://dx.doi.org/10.1016/j.ymben.2006.06.003
|pdf=bionlp-aimed-04.pdf
|pdf=MetabolicEngineering_OneCarbonMetab_2007.pdf
|comment=
|comment=[http://www.marcottelab.org/paper-pdfs/MetabolicEngineering_OneCarbonMetab_2007_SupplementalFile1.xls Supplemental File 1] [http://www.marcottelab.org/paper-pdfs/MetabolicEngineering_OneCarbonMetab_2007_SupplementalFile2.xls Supplemental File 2] [http://www.marcottelab.org/paper-pdfs/MetabolicEngineering_OneCarbonMetab_2007_SupplementalFile3.xls Supplemental File 3]
}}
}}
</li>
</li>
<li value="48"> {{Paper
<li value="60"> {{Paper
|title=Using biomedical literature mining to consolidate the set of known human protein-protein interactions
|title=A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality
|authors=Ramani AK, Marcotte EM, Bunescu RC, Mooney RJ
|authors=Hart GT, Lee I, Marcotte EM
|journal=Intelligent Systems in Molecular Biology-ACL Workshop
|journal=BMC Bioinformatics
|pub_year=2005
|pub_year=2007
|volume=
|volume=8
|page=
|page=236.
|pubmed=  
|pubmed=17605818
|link=
|link=http://www.biomedcentral.com/1471-2105/8/236
|pdf=ISMB-ACLworkshop_LitMining_2005.pdf
|pdf=BMCBioinformatics_YeastComplexEssentiality_2007.pdf
|comment=
|comment=
}}
}}
</li>
</li>
<li value="47"> {{Paper
</ol>
|title=Protein function prediction using the Protein Link Explorer (PLEX)
|authors=Date SV, Marcotte EM
|journal=Bioinformatics
|pub_year=2005
|volume=21(10)
|page=2558-9
|pubmed=15701682 
|link=http://bioinformatics.oxfordjournals.org/cgi/content/full/21/10/2558
|pdf=Plex.pdf
|comment=[http://bioinformatics.icmb.utexas.edu/plex/plex.html Supplemental Web Site]
}}
</li>
</ol>


== 2004 ==
== 2006 ==
<ol>
<ol>
<li value="46"> {{Paper
<li value="59"> {{Paper
|title=A probabilistic functional network of yeast genes
|title=How complete are current yeast and human protein-interaction networks?
|authors=Lee I, Date SV, Adai AT, Marcotte EM
|authors=Hart GT, Ramani AK, Marcotte EM.
|journal=Science
|journal=Genome Biol.
|pub_year=2004
|pub_year=2006
|volume=306(5701)
|volume=7(11)
|page=1555-8
|page=120
|pubmed=15567862
|pubmed=17147767
|pdf=Science_Lee_YeastNet.pdf
|link=http://genomebiology.com/2006/7/11/120
|comment=[http://www.marcottelab.org/paper-pdfs/1099511v2s.pdf Supplemental methods] [http://www.marcottelab.org/paper-pdfs/1099511v2s_list.txt Supplemental README] [http://www.marcottelab.org/paper-pdfs/1099511v2s1.zip Supplemental File 1] [http://www.marcottelab.org/paper-pdfs/1099511v2s2.txt Supplemental File 2] [http://www.marcottelab.org/paper-pdfs/1099511v2s3 Supplemental File 3] [http://www.marcottelab.org/paper-pdfs/1099511v2s4.wrl Supplemental File 4] [http://www.marcottelab.org/paper-pdfs/1099511v2s5.wrl Supplemental File 5] (Files 4 & 5 require a VRML viewer)
|pdf=GenomeBiology_HumanPPIOverview_2006.pdf
|comment=[http://www.marcottelab.org/paper-pdfs/GenomeBiology_HumanPPIOverview_2006_AdditionalDataFile1.pdf Additional Data File 1]
}}
}}
</li>
</li>
<li value="45"> {{Paper
<li value="58"> {{Paper
|authors= Baliga NS, Bonneau R, Facciotti MT, Pan M, Glusman G, Deutsch EW, Shannon P, Chiu Y, Weng RS, Gan RR, Hung P, Date SV, Marcotte E, Hood L, Ng WV
|title=Chromatographic alignment of ESI-LC-MS proteomics datasets by ordered bijective interpolated warping
|title=Genome sequence of <i>Haloarcula marismortui</i>: a halophilic archaeon from the Dead Sea
|authors=Prince JT, Marcotte EM
|journal=Genome Res.
|journal=Anal. Chem.  
|volume=14(11)
|pub_year=2006
|page=2221-34
|volume=78(17)
|pub_year=2004
|page=6140-52
|pubmed=15520287
|pubmed=16944896
|pdf=GenomeResearch_HaloarculumGenome.pdf
|link=http://pubs.acs.org/doi/abs/10.1021/ac0605344
|comment=[[File:GenomeResearchHaloarculaCover2004.jpg||100px|right]]
|pdf=AnalyticalChemistry_OBIWarp_2006.pdf
}}
</li>
<li value="44"> {{Paper
|title=Development through the eyes of functional genomics
|authors=Fraser AG, Marcotte EM
|journal=Curr Opin Genet Dev.
|pub_year=2004
|volume=14(4)
|page=336-42
|pubmed=15261648
|link=http://dx.doi.org/10.1016/j.gde.2004.06.015 
|pdf=COGD_FraserMarcotte_2004.pdf
|comment=
|comment=
}}
}}
</li>
</li>
<li value="43"> {{Paper
<li value="57"> {{Paper
|title=Protein interaction networks from yeast to human
|title=A fast coarse filtering method for peptide identification by mass spectrometry
|authors=Bork P, Jensen LJ, Von Mering C, Ramani AK, Lee I, Marcotte EM
|authors=Ramakrishnan SR, Mao R, Nakorchevskiy AA, Prince JT, Willard WS, Xu W, Marcotte EM, Miranker DP
|journal=Curr Opin Struct Biol
|journal=Bioinformatics
|pub_year=2004
|pub_year=2006
|volume=14(3)
|volume=22(12)
|page=292-9
|page=1524-31
|pubmed=15193308
|pubmed=16585069
|link=http://dx.doi.org/10.1016/j.sbi.2004.05.003   
|link=http://bioinformatics.oxfordjournals.org/cgi/content/full/22/12/1524
|pdf=cosb-review.pdf
|pdf=Bioinformatics_MoBIoSCoarseFilter_2006.pdf
|comment=
|comment=
}}
}}
</li>
</li>
<li value="42"> {{Paper
<li value="56"> {{Paper
|title=LGL: Creating a map of protein function with an algorithm for visualizing very large biological networks
|title=Systematic profiling of cellular phenotypes with spotted cell microarrays reveals new pheromone response genes
|authors=Adai AT, Date SV, Wieland S, Marcotte EM
|authors=Narayanaswamy R, Niu W, Scouras A, Hart GT, Davies J, Ellington AD, Iyer VR, Marcotte EM
|journal=J Mol Biol
|journal=Genome Biol.
|pub_year=2004
|pub_year=2006
|volume=340(1)
|volume=7(1)
|page=179-90
|page=R6
|pubmed=15184029
|pubmed=16507139
|link=http://dx.doi.org/10.1016/j.jmb.2004.04.047 
|link=http://genomebiology.com/2006/7/1/R6
|pdf=jmb-lgl.pdf  
|pdf=GenomeBiology_CellChips_2006.pdf
|comment=[http://bioinformatics.icmb.utexas.edu/lgl/index.html Supplemental Web Site] [http://sourceforge.net/projects/lgl/ Sourceforge Site] For more recent support of LGL, see the LGL guide by [http://clairemcwhite.github.io/lgl-guide/ Claire McWhite] and the latest updates from [http://www.opte.org/lgl/ the Opte Project]
|comment=[http://www.marcottelab.org/paper-pdfs/GenomeBiology_CellChips_Supplement_2006.pdf Supplement] [http://www.marcottelab.org/paper-pdfs/NarayanaswamySupplementalTable1.xls Supplemental Table 1] [http://www.marcottelab.org/paper-pdfs/NarayanaswamySupplementalTable2.xls Supplemental Table 2] [http://www.marcottelab.org/paper-pdfs/NarayanaswamySupplementalTable3.xls Supplemental Table 3] [http://www.marcottelab.org/paper-pdfs/NarayanaswamySupplementalTable4.xls Supplemental Table 4]
}}
}}
</li>
</li>
<li value="41"> {{Paper
<li value="55"> {{Paper
|title=A probabilistic view of gene function
|title=Bioinformatic prediction of yeast gene function
|authors=Fraser AG, Marcotte EM
|authors=Lee I, Narayanaswamy R, Marcotte EM
|journal=Nature Genetics
|journal=Yeast Gene Analysis
|pub_year=2004
|pub_year=2006
|volume=36(6)
|volume=Stansfield, I., ed., Elsevier Press
|page=559-64
|page=
|pubmed=15167932
|link=http://dx.doi.org/10.1038/ng1370 
|pdf=ng-fraser-review.pdf
|comment=
}}
</li>
<li value="40"> {{Paper
|title=Practical computational approaches to infer protein function
|authors=Marcotte EM
|journal=Biosilico
|pub_year=2004
|volume=2
|page=24-29
|pubmed=
|pubmed=
|link=  
|link=
|pdf=Biosilico_Marcotte_2004_proofs.pdf
|pdf=LeeNarayanaswamyMarcotteManuscript.pdf
|comment=
|comment=
}}
}}
</li>
</li>
<li value="39"> {{Paper
<li value="54"> {{Paper
|title=The need for a public proteomics repository
|title=Bioinformatic challenges for the next decade(s)
|authors=Prince JT, Carlson MW, Wang R, Lu P, Marcotte EM
|authors=Eisenberg D, Marcotte E, McLachlan AD, Pellegrini M
|journal=Nature Biotechnology
|journal=Philos Trans R Soc Lond B Biol Sci.
|pub_year=2004
|pub_year=2006
|volume=22(4)
|volume=361(1467)
|page=471-472
|page=525-7
|pubmed=15085804
|pubmed=16524841
|link=http://dx.doi.org/10.1038/nbt0404-471
|link=http://rstb.royalsocietypublishing.org/content/361/1467/525.long
|nbt-MS-review.pdf
|pdf=PhilTransactionsRoyalSocB_BioinformaticChallenges_2006.pdf
|comment=[http://bioinformatics.icmb.utexas.edu/OPD/ Supplemental Web Site]
}}
</li>
<li value="38"> {{Paper
|title=Response to McDermott and Samudrala: Enhanced functional information from predicted protein networks
|authors=Date SV, Marcotte EM
|journal=TRENDS in Biotechnology
|pub_year=2004
|volume=22(2)
|page=62-63
|pubmed=
|link=http://dx.doi.org/10.1016/j.tibtech.2003.11.008 
|pdf=trends-biotech.pdf
|comment=
|comment=
}}
}}
Line 2,662: Line 2,785:
</ol>
</ol>


== 2003 ==
== 2005 ==
<ol>
<ol>
<li value="37"> {{Paper
<li value="53"> {{Paper
|title=Diametrical clustering for identifying anti-correlated gene clusters
|title=Synthetic biology: Engineering ''Escherichia coli'' to see light
|authors=Dhillon IS, Marcotte EM, Roshan U
|authors=Levskaya A, Chevalier AA, Tabor JJ, Simpson ZB, Lavery LA, Levy M, Davidson EA, Scouras A, Ellington AD, Marcotte EM, Voigt CA
|journal=Bioinformatics
|journal=Nature
|pub_year=2003
|pub_year=2005
|volume=19(13)
|volume=438(7067)
|pubmed=12967956
|page=441-2
|page=1612-9
|pubmed=16306980 
|pdf=diametrical.pdf
|link=http://dx.doi.org/10.1038/nature04405
|pdf=Nature_BacterialPhotography_2005.pdf
|comment=[http://www.sciencedaily.com/releases/2005/11/051123171556.htm the Science Daily press release] [http://dx.doi.org/10.1038/4381064a <i>Nature</i> 2005 Gallery "First Glimpse"] [http://dx.doi.org/10.1038/438417a <i>Nature</i> feature on the iGEM competition featuring a bacterial portrait] [http://www.utexas.edu/features/2005/bacteria/ UT press release] [http://www.nytimes.com/2005/11/24/national/24film.html New York Times feature]
}}
}}
</li>
</li>
<li value="36"> {{Paper
<li value="52"> {{Paper
|title=Expression deconvolution: a reinterpretation of DNA microarray data reveals dynamic changes in cell populations
|title=A fast coarse filtering method for protein identification by mass spectrometry
|authors=Lu P, Nakorchevskiy A, Marcotte EM
|authors=Ramakrishnan SR, Mao R, Nakorchevskiy AA, Prince JT, Willard WS, Xu W, Marcotte EM, Miranker DP
|journal=Proc Natl Acad Sci U S A
|journal=University of Texas Dept. of Computer Sciences, Technical Report
|pub_year=2003
|pub_year=2005
|volume=100(18)
|volume=TR-05-06
|page=10370-5
|page=
|pubmed=12934019
|pubmed=  
|pdf=peng-pnas.pdf
|link=
|comment=[http://www.marcottelab.org/paper-pdfs/PNAS_deconvolution_2003-supplementalfiles.zip Supplemental files] (zipped folder containing executable .jar file, yeast test data and cell cycle basis vectors)
|pdf=TechnicalReport-MoBIoS-TR-05-06.pdf
|comment=
}}
}}
</li>
</li>
<li value="35"> {{Paper
<li value="51"> {{Paper
|title=Discovery of uncharacterized cellular systems by genome-wide analysis of functional linkages
|title=Mass spectrometry of the <i>M. smegmatis</i> proteome: Protein expression levels correlate with function, operons, and codon bias
|authors=Date SV, Marcotte EM
|authors=Wang R, Prince JT, Marcotte EM
|journal=Nat Biotechnol.
|journal=Genome Res.
|pub_year=2003
|pub_year=2005
|volume=21(9)
|volume=15(8)
|page=1055-62
|page=1118-26
|pubmed=12923548
|pubmed=16077011
|pdf=shailesh-natbt.pdf
|link=http://genome.cshlp.org/content/15/8/1118.long
|comment=[http://www.marcottelab.org/paper-pdfs/NatureBiotech_SystematicNewPathways_FigS1.pdf Fig S1] [http://www.marcottelab.org/paper-pdfs/NatureBiotech_SystematicNewPathways_FigS2.gif Fig S2] [http://www.marcottelab.org/paper-pdfs/NatureBiotech_SystematicNewPathways_TableS1.pdf Table S1]
|pdf=rong_2005.pdf
|comment=
}}
}}
</li>
</li>
<li value="34"> {{Paper
<li value="50"> {{Paper
|title=Assembling a jigsaw puzzle with 20,000 parts
|title=Consolidating the set of known human protein-protein interactions in preparation for large-scale mapping of the human interactome
|authors=Marcotte EM
|authors=Ramani AK, Bunescu RC, Mooney RJ, Marcotte EM
|journal=Genome Biol.
|journal=Genome Biology
|pub_year=2003
|pub_year=2005
|volume=4(6)
|volume=6(5)
|page=323
|page=R40
|pubmed=12801408
|pubmed=15892868 
|pdf=genome-biology.pdf
|link=http://genomebiology.com/2005/6/5/R40
|pdf=Arun-consolidate-human.pdf
|comment=
}}
}}
</li>
</li>
<li value="33"> {{Paper
<li value="49"> {{Paper
|title=Exploiting the co-evolution of interacting proteins to discover interaction specificity
|title=Comparative experiments on learning information extractors for proteins and their interactions
|authors=Ramani AK, Marcotte EM
|authors=Bunescu R, Ge R, Kate RJ, Marcotte EM, Mooney RJ, Ramani AK, Wong YW
|journal=J Mol Biol.
|journal=Artif Intell Med.
|pub_year=2003
|pub_year=2005
|volume=327(1)
|volume=33(2)
|page=273-84
|page=139-55
|pubmed=12614624
|pubmed=15811782 
|pdf=jmb_2003.pdf
|link=http://dx.doi.org/10.1016/j.artmed.2004.07.016
|comment=[http://orion.icmb.utexas.edu/matrix/ Supplemental Web Site]
|pdf=bionlp-aimed-04.pdf
|comment=
}}
}}
</li>
</li>
<li value="32"> {{Paper
<li value="48"> {{Paper
|title=The genome sequence of the filamentous fungus <i>Neurospora crassa</i>
|title=Using biomedical literature mining to consolidate the set of known human protein-protein interactions
|authors=Galagan JE, Calvo SE, Borkovich KA, Selker EU, Read ND, Jaffe D, FitzHugh W, Ma LJ, Smirnov S, Purcell S, Rehman B, Elkins T, Engels R, Wang S, Nielsen CB, Butler J, Endrizzi M, Qui D, Ianakiev P, Bell-Pedersen D, Nelson MA, Werner-Washburne M, Selitrennikoff CP, Kinsey JA, Braun EL, Zelter A, Schulte U, Kothe GO, Jedd G, Mewes W, Staben C, Marcotte E, Greenberg D, Roy A, Foley K, Naylor J, Stange-Thomann N, Barrett R, Gnerre S, Kamal M, Kamvysselis M, Mauceli E, Bielke C, Rudd S, Frishman D, Krystofova S, Rasmussen C, Metzenberg RL, Perkins DD, Kroken S, Cogoni C, Macino G, Catcheside D, Li W, Pratt RJ, Osmani SA, DeSouza CP, Glass L, Orbach MJ, Berglund JA, Voelker R, Yarden O, Plamann M, Seiler S, Dunlap J, Radford A, Aramayo R, Natvig DO, Alex LA, Mannhaupt G, Ebbole DJ, Freitag M, Paulsen I, Sachs MS, Lander ES, Nusbaum C, Birren B
|authors=Ramani AK, Marcotte EM, Bunescu RC, Mooney RJ
|journal=Nature
|journal=Intelligent Systems in Molecular Biology-ACL Workshop
|pub_year=2003
|pub_year=2005
|volume=422(6934)
|volume=
|page=859-68
|page=
|pubmed=12712197
|pubmed=  
|pdf=Ncrassa.pdf
|link=
|pdf=ISMB-ACLworkshop_LitMining_2005.pdf
|comment=
}}
}}
</li>
</li>
<li value="31"> {{Paper
<li value="47"> {{Paper
|authors=Bunescu R, Ge R, Kate R, Mooney R, Wong Y, Marcotte E, Ramani A
|title=Protein function prediction using the Protein Link Explorer (PLEX)
|title=Learning to extract proteins and their interactions from Medline abstracts
|authors=Date SV, Marcotte EM
|journal=ICML Workshop
|journal=Bioinformatics
|pub_year=2003
|pub_year=2005
|volume=
|volume=21(10)
|page=
|page=2558-9
|pdf=icmlws.pdf
|pubmed=15701682 
|link=http://bioinformatics.oxfordjournals.org/cgi/content/full/21/10/2558
|pdf=Plex.pdf
|comment=[http://bioinformatics.icmb.utexas.edu/plex/plex.html Supplemental Web Site]
}}
}}
</li>
</li>
</ol>
</ol>


== 2002 ==
== 2004 ==
<ol>
<ol>
<li value="30"> {{Paper
<li value="46"> {{Paper
|title=Making sense of proteomics: Using bioinformatics to discover a protein's structure, functions, and interactions
|title=A probabilistic functional network of yeast genes
|authors=Mallick P, Marcotte EM
|authors=Lee I, Date SV, Adai AT, Marcotte EM
|journal=Proteins and Proteomics: A Laboratory Manual
|journal=Science
|pub_year=2002
|pub_year=2004
|volume=Simpson RJ, ed., Cold Spring Harbor Press
|volume=306(5701)
|page=
|page=1555-8
|link=
|pubmed=15567862
|comment=  
|pdf=Science_Lee_YeastNet.pdf
|comment=[http://www.marcottelab.org/paper-pdfs/1099511v2s.pdf Supplemental methods] [http://www.marcottelab.org/paper-pdfs/1099511v2s_list.txt Supplemental README] [http://www.marcottelab.org/paper-pdfs/1099511v2s1.zip Supplemental File 1] [http://www.marcottelab.org/paper-pdfs/1099511v2s2.txt Supplemental File 2] [http://www.marcottelab.org/paper-pdfs/1099511v2s3 Supplemental File 3] [http://www.marcottelab.org/paper-pdfs/1099511v2s4.wrl Supplemental File 4] [http://www.marcottelab.org/paper-pdfs/1099511v2s5.wrl Supplemental File 5] (Files 4 & 5 require a VRML viewer)
}}
}}
</li>
</li>
<li value="29"> {{Paper
<li value="45"> {{Paper
|title=Diametrical clustering for identifying anti-correlated gene clusters
|authors= Baliga NS, Bonneau R, Facciotti MT, Pan M, Glusman G, Deutsch EW, Shannon P, Chiu Y, Weng RS, Gan RR, Hung P, Date SV, Marcotte E, Hood L, Ng WV
|authors=Dhillon IS, Marcotte EM, Roshan U.
|title=Genome sequence of <i>Haloarcula marismortui</i>: a halophilic archaeon from the Dead Sea
|journal=The University of Texas at Austin, Department of Computer Sciences
|journal=Genome Res.
|pub_year=2002
|volume=14(11)
|volume=Technical Report TR-02-49
|page=2221-34
|pubmed=
|pub_year=2004
|page=
|pubmed=15520287
|link=
|pdf=GenomeResearch_HaloarculumGenome.pdf
|comment=
|comment=[[File:GenomeResearchHaloarculaCover2004.jpg||100px|right]]
|pdf=TechnicalReport_DiametricClustering_tr02-49.pdf
}}
}}
</li>
</li>
<li value="28"> {{Paper
<li value="44"> {{Paper
|title=Predicting protein function and networks on genome-wide scale
|title=Development through the eyes of functional genomics
|authors=Marcotte EM
|authors=Fraser AG, Marcotte EM
|journal=Gene Regulation and Metabolism: Post-Genomic Computational Approaches
|journal=Curr Opin Genet Dev.
|pub_year=2002
|pub_year=2004
|volume=Collado-Vides J, Holfstadt R, eds., MIT press
|volume=14(4)
|pubmed=
|page=336-42
|page=
|pubmed=15261648
|link=
|link=http://dx.doi.org/10.1016/j.gde.2004.06.015 
|pdf=COGD_FraserMarcotte_2004.pdf 
|comment=
|comment=
|pdf=Marcotte-ColladoVidesChapter-2002.pdf
}}
}}
</li>
</li>
<li value="27"> {{Paper
<li value="43"> {{Paper
|title=Predicting functional linkages from gene fusions with confidence
|title=Protein interaction networks from yeast to human
|authors=Verjovsky Marcotte CJ, Marcotte EM
|authors=Bork P, Jensen LJ, Von Mering C, Ramani AK, Lee I, Marcotte EM
|journal=Applied Bioinformatics
|journal=Curr Opin Struct Biol
|pub_year=2002
|pub_year=2004
|volume=1(2)
|volume=14(3)
|pubmed=12967956
|page=292-9
|page=1-8
|pubmed=15193308
|link=
|link=http://dx.doi.org/10.1016/j.sbi.2004.05.003   
|pdf=cosb-review.pdf
|comment=
|comment=
|pdf=RS_statistics.pdf
}}
}}
</li>
</li>
</ol>
<li value="42"> {{Paper
 
|title=LGL: Creating a map of protein function with an algorithm for visualizing very large biological networks
== 2001 ==
|authors=Adai AT, Date SV, Wieland S, Marcotte EM
<ol>
|journal=J Mol Biol
<li value="26"> {{Paper
|pub_year=2004
|title=Exploiting big biology: Integrating large-scale biological data for functional inference
|volume=340(1)
|authors=Marcotte EM, Date SV
|page=179-90
|journal=Brief Bioinform
|pubmed=15184029
|pub_year=2001
|link=http://dx.doi.org/10.1016/j.jmb.2004.04.047 
|volume=2(4)
|pdf=jmb-lgl.pdf 
|page=363-74
|comment=[http://bioinformatics.icmb.utexas.edu/lgl/index.html Supplemental Web Site] [http://sourceforge.net/projects/lgl/ Sourceforge Site] For more recent support of LGL, see the LGL guide by [http://clairemcwhite.github.io/lgl-guide/ Claire McWhite] and the latest updates from [http://www.opte.org/lgl/ the Opte Project]
|pubmed=11808748
}}
|link=
</li>
|pdf=BIB_review.pdf
<li value="41"> {{Paper
|title=A probabilistic view of gene function
|authors=Fraser AG, Marcotte EM
|journal=Nature Genetics
|pub_year=2004
|volume=36(6)
|page=559-64
|pubmed=15167932
|link=http://dx.doi.org/10.1038/ng1370 
|pdf=ng-fraser-review.pdf
|comment=
|comment=
}}
}}
</li>
</li>
<li value="25"> {{Paper
<li value="40"> {{Paper
|title=The path not taken
|title=Practical computational approaches to infer protein function
|authors=Marcotte EM
|authors=Marcotte EM
|journal=Nature Biotechnology
|journal=Biosilico
|pub_year=2001
|pub_year=2004
|volume=19(7)
|volume=2
|page=626-7
|page=24-29
|pubmed=11433271
|pubmed=
|link=
|link=  
|pdf=path-not-taken.pdf
|pdf=Biosilico_Marcotte_2004_proofs.pdf
|comment=
|comment=
}}
}}
</li>
</li>
<li value="24"> {{Paper
<li value="39"> {{Paper
|title=Measuring the dynamics of the proteome
|title=The need for a public proteomics repository
|authors=Marcotte EM
|authors=Prince JT, Carlson MW, Wang R, Lu P, Marcotte EM
|journal=Genome Research
|journal=Nature Biotechnology
|pub_year=2001
|pub_year=2004
|volume=11(2)
|volume=22(4)
|page=191-3
|page=471-472
|pubmed=11157781
|pubmed=15085804
|link=
|link=http://dx.doi.org/10.1038/nbt0404-471
|pdf=measuring-dynamics.pdf
|nbt-MS-review.pdf
|comment=
|comment=[http://bioinformatics.icmb.utexas.edu/OPD/ Supplemental Web Site]
}}
}}
</li>
</li>
<li value="23"> {{Paper
<li value="38"> {{Paper
|title=Mining literature for protein interactions
|title=Response to McDermott and Samudrala: Enhanced functional information from predicted protein networks
|authors=Marcotte EM, Xenarios I, Eisenberg D
|authors=Date SV, Marcotte EM
|journal=Bioinformatics
|journal=TRENDS in Biotechnology
|pub_year=2001
|pub_year=2004
|volume=17(4)
|volume=22(2)
|page=359-63
|page=62-63
|pubmed=11301305
|pubmed=
|link=
|link=http://dx.doi.org/10.1016/j.tibtech.2003.11.008 
|pdf=Bioinformatics_lit_mining.pdf
|pdf=trends-biotech.pdf
|comment=[http://www.marcottelab.org/paper-pdfs/README README] [http://www.marcottelab.org/paper-pdfs/500_abstracts_with_PMID 500_abstracts_with_PMID] [http://www.marcottelab.org/paper-pdfs/Discriminating_words_for_interactions Discriminating_words_for_interactions] [http://www.marcottelab.org/paper-pdfs/Discriminating_words_for_interactions_edited Discriminating_words_for_interactions_edited] [http://www.marcottelab.org/paper-pdfs/score_abstracts score_abstracts Perl script]
}}
</li>
<li value="22"> {{Paper
|title=From genome sequences to protein interactions
|authors=Eisenberg D, Marcotte E, Pellegrini M, Thompson M, Xenarios I, Yeates T
|journal=FASEB J
|pub_year=2001
|volume=15
|page=A724-A724
|pubmed=
|link=
|pdf=
|comment=
|comment=
}}
}}
</li>
</li>
<li value="21"> {{Paper
</ol>
|title=DIP: the database of interacting proteins: 2001 update
 
|authors=Xenarios I, Fernandez E, Salwinski L, Duan XJ, Thompson MJ, Marcotte EM, Eisenberg D
== 2003 ==
|journal=Nucleic Acids Res
<ol>
|pub_year=2001
<li value="37"> {{Paper
|volume=29(1)
|title=Diametrical clustering for identifying anti-correlated gene clusters
|page=239-41
|authors=Dhillon IS, Marcotte EM, Roshan U
|pubmed=11125102
|journal=Bioinformatics
|link=
|pub_year=2003
|pdf=NAR_DIP_2001.pdf
|volume=19(13)
|comment=
|pubmed=12967956
|page=1612-9
|pdf=diametrical.pdf
}}
}}
</li>
</li>
</ol>
<li value="36"> {{Paper
 
|title=Expression deconvolution: a reinterpretation of DNA microarray data reveals dynamic changes in cell populations
== 2000 ==
|authors=Lu P, Nakorchevskiy A, Marcotte EM
<ol>
|journal=Proc Natl Acad Sci U S A
<li value="20"> {{Paper
|pub_year=2003
|title=Protein function in the post-genomic era
|volume=100(18)
|authors=Eisenberg D, Marcotte EM, Xenarios I, Yeates TO
|page=10370-5
|journal=Nature
|pubmed=12934019
|pub_year=2000
|pdf=peng-pnas.pdf
|volume=405(6788)
|comment=[http://www.marcottelab.org/paper-pdfs/PNAS_deconvolution_2003-supplementalfiles.zip Supplemental files] (zipped folder containing executable .jar file, yeast test data and cell cycle basis vectors)
|page=823-6
}}
|pubmed=10866208
|link=http://dx.doi.org/10.1038/35015694
|pdf=Nature_Review_2000.taf
|comment=
}}
</li>
</li>
<li value="19"> {{Paper
<li value="35"> {{Paper
|title=Localizing proteins in the cell from their phylogenetic profiles
|title=Discovery of uncharacterized cellular systems by genome-wide analysis of functional linkages
|authors=Marcotte EM, Xenarios I, van der Bliek A, Eisenberg D
|authors=Date SV, Marcotte EM
|journal=Proc Natl Acad Sci U S A.
|journal=Nat Biotechnol.
|pub_year=2000
|pub_year=2003
|volume=97(22)
|volume=21(9)
|page=12115-20
|page=1055-62
|pubmed=11035803
|pubmed=12923548
|link=http://www.pnas.org/content/97/22/12115.long
|pdf=shailesh-natbt.pdf
|pdf=PNAS_mito_profiles.pdf
|comment=[http://www.marcottelab.org/paper-pdfs/NatureBiotech_SystematicNewPathways_FigS1.pdf Fig S1] [http://www.marcottelab.org/paper-pdfs/NatureBiotech_SystematicNewPathways_FigS2.gif Fig S2] [http://www.marcottelab.org/paper-pdfs/NatureBiotech_SystematicNewPathways_TableS1.pdf Table S1]
|comment=
}}
}}
</li>
</li>
<li value="18"> {{Paper
<li value="34"> {{Paper
|title=Computational genetics: Finding function by non-homology methods
|title=Assembling a jigsaw puzzle with 20,000 parts
|authors=Marcotte EM
|authors=Marcotte EM
|journal=Curr Opin Struct Biol.  
|journal=Genome Biol.
|pub_year=2000
|pub_year=2003
|volume=10(3)
|volume=4(6)
|page=359-65
|page=323
|pubmed=10851184
|pubmed=12801408
|link=http://dx.doi.org/10.1016/S0959-440X(00)00097-X   
|pdf=genome-biology.pdf
|pdf=cosb_compgenetics_2000.pdf
|comment=
}}
}}
</li>
</li>
<li value="17"> {{Paper
<li value="33"> {{Paper
|title=Characterization of a thermostable DNA glycosylase specific for U/G and T/G mismatches from the hyperthermophilic archaeon <i>Pyrobaculum aerophilum</i>
|title=Exploiting the co-evolution of interacting proteins to discover interaction specificity
|authors=Yang H, Fitz-Gibbon S, Marcotte EM, Tai JH, Hyman EC, Miller JH
|authors=Ramani AK, Marcotte EM
|journal=J Bacteriol.
|journal=J Mol Biol.
|pub_year=2000
|pub_year=2003
|volume=182(5)
|volume=327(1)
|page=1272-9
|page=273-84
|pubmed=10671447
|pubmed=12614624
|link=http://jb.asm.org/cgi/content/full/182/5/1272?view=long&pmid=10671447
|pdf=jmb_2003.pdf
|pdf=JBacti_Pyrobaculum_glycosylase.pdf
|comment=[http://orion.icmb.utexas.edu/matrix/ Supplemental Web Site]
|comment=
}}
}}
</li>
</li>
<li value="16"> {{Paper
<li value="32"> {{Paper
|title=Increasing the specificity of protein functional inference by the Rosetta Stone method
|title=The genome sequence of the filamentous fungus <i>Neurospora crassa</i>
|authors=Thompson M, Marcotte E, Pellegrini M, Yeates T, Eisenberg D
|authors=Galagan JE, Calvo SE, Borkovich KA, Selker EU, Read ND, Jaffe D, FitzHugh W, Ma LJ, Smirnov S, Purcell S, Rehman B, Elkins T, Engels R, Wang S, Nielsen CB, Butler J, Endrizzi M, Qui D, Ianakiev P, Bell-Pedersen D, Nelson MA, Werner-Washburne M, Selitrennikoff CP, Kinsey JA, Braun EL, Zelter A, Schulte U, Kothe GO, Jedd G, Mewes W, Staben C, Marcotte E, Greenberg D, Roy A, Foley K, Naylor J, Stange-Thomann N, Barrett R, Gnerre S, Kamal M, Kamvysselis M, Mauceli E, Bielke C, Rudd S, Frishman D, Krystofova S, Rasmussen C, Metzenberg RL, Perkins DD, Kroken S, Cogoni C, Macino G, Catcheside D, Li W, Pratt RJ, Osmani SA, DeSouza CP, Glass L, Orbach MJ, Berglund JA, Voelker R, Yarden O, Plamann M, Seiler S, Dunlap J, Radford A, Aramayo R, Natvig DO, Alex LA, Mannhaupt G, Ebbole DJ, Freitag M, Paulsen I, Sachs MS, Lander ES, Nusbaum C, Birren B
|journal=Currents in Computational Molecular Biology
|journal=Nature
|pub_year=2000
|pub_year=2003
|volume=Miyano S, Shamir R, Takagi T, eds., Universal Academy Press, Inc.
|volume=422(6934)
|page=
|page=859-68
|pubmed=
|pubmed=12712197
|link=
|pdf=Ncrassa.pdf
|pdf=CurrentsinCompMolBio_Thompson_2000.pdf
|comment=
}}
}}
</li>
</li>
<li value="15"> {{Paper
<li value="31"> {{Paper
|title=DIP: the database of interacting proteins
|authors=Bunescu R, Ge R, Kate R, Mooney R, Wong Y, Marcotte E, Ramani A
|authors=Xenarios I, Rice DW, Salwinski L, Baron MK, Marcotte EM, Eisenberg D
|title=Learning to extract proteins and their interactions from Medline abstracts
|journal=Nucleic Acids Res.
|journal=ICML Workshop
|pub_year=2000
|pub_year=2003
|volume=28(1)
|volume=
|page=289-91
|page=
|pubmed=10592249
|pdf=icmlws.pdf
|link=http://nar.oxfordjournals.org/cgi/content/full/28/1/289
|pdf=NAR_DIP_2000.pdf
|comment=
}}
}}
</li>
</li>
</ol>
</ol>


== 1999 ==
== 2002 ==
<ol>
<ol>
<li value="14"> {{Paper
<li value="30"> {{Paper
|title=A combined algorithm for genome-wide prediction of protein function
|title=Making sense of proteomics: Using bioinformatics to discover a protein's structure, functions, and interactions
|authors=Marcotte EM, Pellegrini M, Thompson MJ, Yeates TO, Eisenberg D
|authors=Mallick P, Marcotte EM
|journal=Nature
|journal=Proteins and Proteomics: A Laboratory Manual
|pub_year=1999
|pub_year=2002
|volume=402(6757)
|volume=Simpson RJ, ed., Cold Spring Harbor Press
|page=83-6
|page=
|pubmed=10573421
|link=
|link=http://www.nature.com/nature/journal/v402/n6757/full/402083a0.html
|comment=  
|pdf=nature_genomewidepred.pdf
|comment=See also Sali, A.  Genomics: Functional links between proteins.  Nature 402, 23-26 (1999), Boston Globe (Nov. 3, 1999), Los Angeles Times (Nov. 4, 1999).
}}
}}
</li>
</li>
<li value="13"> {{Paper
<li value="29"> {{Paper
|title=Detecting protein function and protein-protein interactions from genome sequences
|title=Diametrical clustering for identifying anti-correlated gene clusters
|authors=Marcotte EM, Pellegrini M, Ng HL, Rice DW, Yeates TO, Eisenberg D
|authors=Dhillon IS, Marcotte EM, Roshan U.
|journal=Science
|journal=The University of Texas at Austin, Department of Computer Sciences
|pub_year=1999
|pub_year=2002
|volume=285(5428)
|volume=Technical Report TR-02-49
|page=751-3
|pubmed=
|pubmed=10427000
|page=
|link=http://dx.doi.org/10.1126/science.285.5428.751
|link=
|pdf=RS_science.pdf
|comment=
|comment=See also Doolittle, R. F.  Do you dig my groove? Nature: Genetics  23, 6-8 (1999).
|pdf=TechnicalReport_DiametricClustering_tr02-49.pdf
}}
}}
</li>
</li>
<li value="12"> {{Paper
<li value="28"> {{Paper
|title=A census of protein repeats
|title=Predicting protein function and networks on genome-wide scale
|authors=Marcotte EM, Pellegrini M, Yeates TO, Eisenberg D
|authors=Marcotte EM
|journal=J Mol Biol.
|journal=Gene Regulation and Metabolism: Post-Genomic Computational Approaches
|pub_year=1999
|pub_year=2002
|volume=293(1)
|volume=Collado-Vides J, Holfstadt R, eds., MIT press
|page=151-60
|pubmed=
|pubmed=10512723
|page=
|link=http://dx.doi.org/10.1006/jmbi.1999.3136   
|link=
|pdf=JMB_Census_2000.pdf
|comment=
|comment=
|pdf=Marcotte-ColladoVidesChapter-2002.pdf
}}
}}
</li>
</li>
<li value="11"> {{Paper
<li value="27"> {{Paper
|title=Assigning protein functions by comparative genome analysis: protein phylogenetic profiles
|title=Predicting functional linkages from gene fusions with confidence
|authors=Pellegrini M, Marcotte EM, Thompson MJ, Eisenberg D, Yeates TO
|authors=Verjovsky Marcotte CJ, Marcotte EM
|journal=Proc Natl Acad Sci U S A
|journal=Applied Bioinformatics
|pub_year=1999
|pub_year=2002
|volume=96(8)
|volume=1(2)
|page=4285-8
|pubmed=12967956
|pubmed=10200254
|page=1-8
|link=http://www.pnas.org/content/96/8/4285.long
|link=
|pdf=PNAS_phylogenetic_profiles.pdf
|comment=
}}
</li>
<li value="10"> {{Paper
|title=A fast algorithm for genome-wide analysis of proteins with repeated sequences
|authors=Pellegrini M, Marcotte EM, Yeates TO
|journal=Proteins: Struct. Funct. Genet.
|pub_year=1999
|volume=35(4)
|page=440-6
|pubmed=10382671
|link=http://www3.interscience.wiley.com/journal/65000326/abstract?CRETRY=1&SRETRY=0
|pdf=Proteins_repeats_in_proteins.pdf
|comment=
|comment=
|pdf=RS_statistics.pdf
}}
}}
</li>
</li>
</ol>
</ol>


== 1998 ==
== 2001 ==
<ol>
<ol>
<li value="9"> {{Paper
<li value="26"> {{Paper
|title=Chicken prion tandem repeats form a stable, protease-resistant domain
|title=Exploiting big biology: Integrating large-scale biological data for functional inference
|authors=Marcotte EM, Eisenberg D
|authors=Marcotte EM, Date SV
|journal=Biochemistry
|journal=Brief Bioinform
|pub_year=1998
|pub_year=2001
|volume=38(2)
|volume=2(4)
|page=667-76
|page=363-74
|pubmed=9888807
|pubmed=11808748
|link=http://dx.doi.org/10.1021/bi981487f
|link=
|pdf=chickenprion.pdf
|pdf=BIB_review.pdf
|comment=
}}
</li>
<li value="25"> {{Paper
|title=The path not taken
|authors=Marcotte EM
|journal=Nature Biotechnology
|pub_year=2001
|volume=19(7)
|page=626-7
|pubmed=11433271
|link=
|pdf=path-not-taken.pdf
|comment=
|comment=
}}
}}
</li>
</li>
<li value="8"> {{Paper
<li value="24"> {{Paper
|title=A look at the future of macromolecular structure determination
|title=Measuring the dynamics of the proteome
|authors=Cascio D, Goodwill K, Marcotte E
|authors=Marcotte EM
|journal=Rigaku J.
|journal=Genome Research
|pub_year=1998
|pub_year=2001
|volume=15
|volume=11(2)
|page=1-5
|page=191-3
|pubmed=
|pubmed=11157781
|link=
|link=
|pdf=RigakuJournal_look_at_xtal_future.pdf
|pdf=measuring-dynamics.pdf
|comment=
|comment=
}}
}}
</li>
</li>
<li value="7"> {{Paper
<li value="23"> {{Paper
|title=Structural analysis shows five glycohydrolase families diverged from a common ancestor
|title=Mining literature for protein interactions
|authors=Robertus JD, Monzingo AF, Marcotte EM, Hart PJ
|authors=Marcotte EM, Xenarios I, Eisenberg D
|journal=J Exp Zool.
|journal=Bioinformatics
|pub_year=1998
|pub_year=2001
|volume=282(1-2)
|volume=17(4)
|page=127-32
|page=359-63
|pubmed=9723170
|pubmed=11301305
|link=http://www3.interscience.wiley.com/journal/75837/abstract
|link=
|pdf=JExpZool_chitinase_evolution.pdf
|pdf=Bioinformatics_lit_mining.pdf
|comment=[http://www.marcottelab.org/paper-pdfs/README README] [http://www.marcottelab.org/paper-pdfs/500_abstracts_with_PMID 500_abstracts_with_PMID] [http://www.marcottelab.org/paper-pdfs/Discriminating_words_for_interactions Discriminating_words_for_interactions] [http://www.marcottelab.org/paper-pdfs/Discriminating_words_for_interactions_edited Discriminating_words_for_interactions_edited] [http://www.marcottelab.org/paper-pdfs/score_abstracts score_abstracts Perl script]
}}
</li>
<li value="22"> {{Paper
|title=From genome sequences to protein interactions
|authors=Eisenberg D, Marcotte E, Pellegrini M, Thompson M, Xenarios I, Yeates T
|journal=FASEB J
|pub_year=2001
|volume=15
|page=A724-A724
|pubmed=
|link=
|pdf=
|comment=
|comment=
}}
}}
</li>
</li>
</ol>
<li value="21"> {{Paper
 
|title=DIP: the database of interacting proteins: 2001 update
== Pre - 1998 ==
|authors=Xenarios I, Fernandez E, Salwinski L, Duan XJ, Thompson MJ, Marcotte EM, Eisenberg D
<ol>
|journal=Nucleic Acids Res
|pub_year=2001
|volume=29(1)
|page=239-41
|pubmed=11125102
|link=
|pdf=NAR_DIP_2001.pdf
|comment=
}}
</li>
</ol>


<li value="6"> {{Paper
== 2000 ==
|title=Kinetic analysis of barley chitinase
<ol>
|authors=Hollis T, Honda Y, Fukamizo T, Marcotte E, Day PJ, Robertus JD
<li value="20"> {{Paper
|journal=Arch Biochem Biophys.
|title=Protein function in the post-genomic era
|pub_year=1997
|authors=Eisenberg D, Marcotte EM, Xenarios I, Yeates TO
|volume=344(2)
|journal=Nature
|page=335-42
|pub_year=2000
|pubmed=9264547
|volume=405(6788)
|link=http://dx.doi.org/10.1006/abbi.1997.0225 
|page=823-6
|pdf=ArchBiochemBiophys_chitinase_kinetics.pdf
|pubmed=10866208
|link=http://dx.doi.org/10.1038/35015694
|pdf=Nature_Review_2000.taf
|comment=
|comment=
}}
}}
</li>
</li>
<li value="5"> {{Paper
<li value="19"> {{Paper
|title=X-ray structure of an anti-fungal chitosanase from <i>Streptomyces</i> N174
|title=Localizing proteins in the cell from their phylogenetic profiles
|authors=Marcotte EM, Monzingo AF, Ernst SR, Brzezinski R, Robertus JD
|authors=Marcotte EM, Xenarios I, van der Bliek A, Eisenberg D
|journal=Nat Struct Biol.
|journal=Proc Natl Acad Sci U S A.
|pub_year=1996
|pub_year=2000
|volume=3(2)
|volume=97(22)
|page=155-62
|page=12115-20
|pubmed=8564542
|pubmed=11035803
|link=
|link=http://www.pnas.org/content/97/22/12115.long
|pdf=NatureStructuralBiology_Chitosanase_1996.pdf
|pdf=PNAS_mito_profiles.pdf
|comment=[http://www.marcottelab.org/paper-pdfs/NatureStructuralBiology_ChitosanaseCommentary_1996.pdf News & Views]
|comment=
}}
}}
</li>
</li>
<li value="4"> {{Paper
<li value="18"> {{Paper
|title=Chitinases, chitosanases, and lysozymes can be divided into procaryotic and eucaryotic families sharing a conserved core
|title=Computational genetics: Finding function by non-homology methods
|authors=Monzingo AF, Marcotte EM, Hart PJ, Robertus JD
|authors=Marcotte EM
|journal=Nat Struct Biol
|journal=Curr Opin Struct Biol.
|pub_year=1996
|pub_year=2000
|volume=3(2)
|volume=10(3)
|page=133-40
|page=359-65
|pubmed=8564539
|pubmed=10851184
|link=
|link=http://dx.doi.org/10.1016/S0959-440X(00)00097-X   
|pdf=NatureStructuralBiology_ConservedCore_1996.pdf
|pdf=cosb_compgenetics_2000.pdf
|comment=
|comment=
}}
}}
</li>
</li>
<li value="3"> {{Paper
<li value="17"> {{Paper
|title=The structure of chitinases and prospects for structure-Based drug design
|title=Characterization of a thermostable DNA glycosylase specific for U/G and T/G mismatches from the hyperthermophilic archaeon <i>Pyrobaculum aerophilum</i>
|authors=Robertus, J. D., Hart, P. J., Monzingo, A. F., Marcotte, E. & Hollis, T
|authors=Yang H, Fitz-Gibbon S, Marcotte EM, Tai JH, Hyman EC, Miller JH
|journal=Can. J. Bot.
|journal=J Bacteriol.
|pub_year=1995
|pub_year=2000
|volume=73 (Suppl. 1)
|volume=182(5)
|page=S1142-S1146
|page=1272-9
|pdf=CanadianJournalOfBotany_Chitinase_1995.pdf
|pubmed=10671447
|link=http://jb.asm.org/cgi/content/full/182/5/1272?view=long&pmid=10671447
|pdf=JBacti_Pyrobaculum_glycosylase.pdf
|comment=
}}
</li>
<li value="16"> {{Paper
|title=Increasing the specificity of protein functional inference by the Rosetta Stone method
|authors=Thompson M, Marcotte E, Pellegrini M, Yeates T, Eisenberg D
|journal=Currents in Computational Molecular Biology
|pub_year=2000
|volume=Miyano S, Shamir R, Takagi T, eds., Universal Academy Press, Inc.
|page=
|pubmed=
|pubmed=
|link=
|link=
|pdf=CurrentsinCompMolBio_Thompson_2000.pdf
|comment=
|comment=
}}
}}
</li>
<li value="15"> {{Paper
|title=DIP: the database of interacting proteins
|authors=Xenarios I, Rice DW, Salwinski L, Baron MK, Marcotte EM, Eisenberg D
|journal=Nucleic Acids Res.
|pub_year=2000
|volume=28(1)
|page=289-91
|pubmed=10592249
|link=http://nar.oxfordjournals.org/cgi/content/full/28/1/289
|pdf=NAR_DIP_2000.pdf
|comment=
}}
</li>
</ol>
 
== 1999 ==
<ol>
<li value="14"> {{Paper
|title=A combined algorithm for genome-wide prediction of protein function
|authors=Marcotte EM, Pellegrini M, Thompson MJ, Yeates TO, Eisenberg D
|journal=Nature
|pub_year=1999
|volume=402(6757)
|page=83-6
|pubmed=10573421
|link=http://www.nature.com/nature/journal/v402/n6757/full/402083a0.html
|pdf=nature_genomewidepred.pdf
|comment=See also Sali, A.  Genomics: Functional links between proteins.  Nature 402, 23-26 (1999), Boston Globe (Nov. 3, 1999), Los Angeles Times (Nov. 4, 1999).
}}
</li>
<li value="13"> {{Paper
|title=Detecting protein function and protein-protein interactions from genome sequences
|authors=Marcotte EM, Pellegrini M, Ng HL, Rice DW, Yeates TO, Eisenberg D
|journal=Science
|pub_year=1999
|volume=285(5428)
|page=751-3
|pubmed=10427000
|link=http://dx.doi.org/10.1126/science.285.5428.751
|pdf=RS_science.pdf
|comment=See also Doolittle, R. F.  Do you dig my groove? Nature: Genetics  23, 6-8 (1999).
}}
</li>
<li value="12"> {{Paper
|title=A census of protein repeats
|authors=Marcotte EM, Pellegrini M, Yeates TO, Eisenberg D
|journal=J Mol Biol.
|pub_year=1999
|volume=293(1)
|page=151-60
|pubmed=10512723
|link=http://dx.doi.org/10.1006/jmbi.1999.3136   
|pdf=JMB_Census_2000.pdf
|comment=
}}
</li>
<li value="11"> {{Paper
|title=Assigning protein functions by comparative genome analysis: protein phylogenetic profiles
|authors=Pellegrini M, Marcotte EM, Thompson MJ, Eisenberg D, Yeates TO
|journal=Proc Natl Acad Sci U S A
|pub_year=1999
|volume=96(8)
|page=4285-8
|pubmed=10200254
|link=http://www.pnas.org/content/96/8/4285.long
|pdf=PNAS_phylogenetic_profiles.pdf
|comment=
}}
</li>
<li value="10"> {{Paper
|title=A fast algorithm for genome-wide analysis of proteins with repeated sequences
|authors=Pellegrini M, Marcotte EM, Yeates TO
|journal=Proteins: Struct. Funct. Genet.
|pub_year=1999
|volume=35(4)
|page=440-6
|pubmed=10382671
|link=http://www3.interscience.wiley.com/journal/65000326/abstract?CRETRY=1&SRETRY=0
|pdf=Proteins_repeats_in_proteins.pdf
|comment=
}}
</li>
</ol>
 
== 1998 ==
<ol>
<li value="9"> {{Paper
|title=Chicken prion tandem repeats form a stable, protease-resistant domain
|authors=Marcotte EM, Eisenberg D
|journal=Biochemistry
|pub_year=1998
|volume=38(2)
|page=667-76
|pubmed=9888807
|link=http://dx.doi.org/10.1021/bi981487f
|pdf=chickenprion.pdf
|comment=
}}
</li>
<li value="8"> {{Paper
|title=A look at the future of macromolecular structure determination
|authors=Cascio D, Goodwill K, Marcotte E
|journal=Rigaku J.
|pub_year=1998
|volume=15
|page=1-5
|pubmed=
|link=
|pdf=RigakuJournal_look_at_xtal_future.pdf
|comment=
}}
</li>
<li value="7"> {{Paper
|title=Structural analysis shows five glycohydrolase families diverged from a common ancestor
|authors=Robertus JD, Monzingo AF, Marcotte EM, Hart PJ
|journal=J Exp Zool.
|pub_year=1998
|volume=282(1-2)
|page=127-32
|pubmed=9723170
|link=http://www3.interscience.wiley.com/journal/75837/abstract
|pdf=JExpZool_chitinase_evolution.pdf
|comment=
}}
</li>
</ol>
 
== Pre - 1998 ==
<ol>
 
<li value="6"> {{Paper
|title=Kinetic analysis of barley chitinase
|authors=Hollis T, Honda Y, Fukamizo T, Marcotte E, Day PJ, Robertus JD
|journal=Arch Biochem Biophys.
|pub_year=1997
|volume=344(2)
|page=335-42
|pubmed=9264547
|link=http://dx.doi.org/10.1006/abbi.1997.0225 
|pdf=ArchBiochemBiophys_chitinase_kinetics.pdf
|comment=
}}
</li>
<li value="5"> {{Paper
|title=X-ray structure of an anti-fungal chitosanase from <i>Streptomyces</i> N174
|authors=Marcotte EM, Monzingo AF, Ernst SR, Brzezinski R, Robertus JD
|journal=Nat Struct Biol.
|pub_year=1996
|volume=3(2)
|page=155-62
|pubmed=8564542
|link=
|pdf=NatureStructuralBiology_Chitosanase_1996.pdf
|comment=[http://www.marcottelab.org/paper-pdfs/NatureStructuralBiology_ChitosanaseCommentary_1996.pdf News & Views]
}}
</li>
<li value="4"> {{Paper
|title=Chitinases, chitosanases, and lysozymes can be divided into procaryotic and eucaryotic families sharing a conserved core
|authors=Monzingo AF, Marcotte EM, Hart PJ, Robertus JD
|journal=Nat Struct Biol
|pub_year=1996
|volume=3(2)
|page=133-40
|pubmed=8564539
|link=
|pdf=NatureStructuralBiology_ConservedCore_1996.pdf
|comment=
}}
</li>
<li value="3"> {{Paper
|title=The structure of chitinases and prospects for structure-Based drug design
|authors=Robertus, J. D., Hart, P. J., Monzingo, A. F., Marcotte, E. & Hollis, T
|journal=Can. J. Bot.
|pub_year=1995
|volume=73 (Suppl. 1)
|page=S1142-S1146
|pdf=CanadianJournalOfBotany_Chitinase_1995.pdf
|pubmed=
|link=
|comment=
}}
</li>
<li value="2"> {{Paper
|title=Control of cellular morphogenesis by the Ip12/Bem2 GTPase-activating protein: possible role of protein phosphorylation
|authors=Kim YJ, Francisco L, Chen GC, Marcotte E, Chan CS
|journal=J Cell Biol.
|pub_year=1994
|volume=127(5)
|page=1381-94
|pubmed=7962097
|link=http://jcb.rupress.org/cgi/reprint/127/5/1381
|pdf=JCellBiol_KimChan_Ipl2Bem2_1994.pdf
|comment=
}}
</li>
<li value="1"> {{Paper
|title=Crystallization of a chitosanase from <i>Streptomyces</i> N174
|authors=Marcotte E, Hart PJ, Boucher I, Brzezinski R, Robertus JD
|journal=J Mol Biol
|pub_year=1993
|volume=232(3)
|page=995-6
|pubmed=8355284
|link=http://dx.doi.org/10.1006/jmbi.1993.1447
|pdf=JMB_chitosanase_xtal_1993.pdf
|comment=
}}
</li>
</ol>
 
== Patents ==
<ol>
<li value="23"> [https://patents.google.com/patent/WO2021236716A2/en WO2021236716A2] '''Methods, systems and kits for polypeptide processing and analysis'''. Priority to US18/056,970. Converted to PCT; published as WO2021236716A2 on November 25, 2021 and as WO2021236716A3 on June 23, 2022. US application filed November 18, 2022 and published as US 2024/0002925 A1 on January 4, 2024.</li>
<li value="22"> [https://patents.google.com/patent/US20240125805A1/en # 63/153,285] '''Methods for polypeptide processing and analysis'''. PCT filed February 24, 2022 with serial number PCT/US2022/017642, published as US 2024/0125805 A1 on April 18, 2024. Chinese Patent Application published on 11/17/2023 under No. CN 117083391 A. European patent application published 1/3/2024 under Publication No. 4298235.</li>
<li value="21"> [https://patents.google.com/patent/US20240168034A1/en # 63/193,328] '''Capture and analysis of proteins from single cells'''. PCT filed May 26, 2022 with serial number PCT/US2022/031022. US patent application US2024/0168034 A1 published as '''Methods and systems for single cell protein analysis''' May 23, 2024. </li>
<li value="20"> [https://www.freepatentsonline.com/y2024/0201198.html # 63/193,436] '''Composition, methods and utility of conjugated biomolecule barcodes'''. PCT filed May 26, 2022 with serial number PCT/US22/31079. US patent application 2024/0201198 A1 published June 20, 2024.</li>
<li value="19"> [https://patents.google.com/patent/WO2022192661A1/en WO2022192661A1] '''Sars-cov-2 neutralizing antibodies and uses thereof '''. PCT filed March 11, 2022 and published as WO2022192661A1 on September 15, 2022.</li>
<li value="18"> [https://patents.google.com/patent/WO2021236716A2 Publication # WO 2021236716 A2] '''Methods, systems and kits for polypeptide processing and analysis'''. PCT filed May 19, 2021.</li>
<li value="17"> [https://patents.google.com/patent/WO2021168083A1 Publication # WO 2021168083 A1] '''Peptide and protein c-terminus labeling'''. Converted to PCT on 2/18/2021 with serial number PCT/US2021/018535. Japanese Patent Application published 4/5/2023 under Publication No. 2023-514316.</li>
<li value="16"> [https://patents.google.com/patent/WO2020072907A1 Publication # WO 2020072907 A1] '''Solid-phase N-terminal peptide capture and release'''. PCT filed Oct 04, 2019.</li>
<li value="15"> [https://patents.google.com/patent/WO2020037046A1 Publication # WO 2020037046 A1] '''Single molecule sequencing peptides bound to the major histocompatibility complex'''. PCT filed Aug 14, 2019. [https://patents.google.com/patent/GB2591384B/en UK patent GB 2591384 B] issued July 26, 2023. [https://patents.google.com/patent/GB2607829B/en UK patent GB 2607829 B] issued August 30, 2023.</li>
<li value="14"> [https://patents.google.com/patent/WO2020023488A1/ Publication # WO 2020023488 A1] '''Single molecule sequencing identification of post-translational modifications on proteins'''. PCT filed July 23, 2018.</li>
<li value="13"> [https://patents.google.com/patent/WO2020014586A1/ Publication # WO 2020014586 A1] '''Molecular neighborhood detection by oligonucleotides'''. PCT filed July 12, 2018.</li>
<li value="12">  [https://patents.google.com/patent/US10175249B2 10,175,249 B2], issued January 8, 2019. '''Proteomic identification of antibodies'''. Lavinder, Jason; Boutz, Danny; Wine, Yariv; Marcotte, Edward; Georgiou, George.  </li>
<li value="11">  [https://patents.google.com/patent/US10545153B2/ 10,545,153 B2], issued January 28, 2020. '''Single molecule peptide sequencing'''. [https://patentscope.wipo.int/search/en/detail.jsf?docId=WO2016069124 Publication # WO/2016/069124], Intl appl # PCT/US2015/050099, International filing date 15.09.2015. Marcotte, Edward; Anslyn, Eric; Ellington, Andrew;  Swaminathan, Jagannath; Hernandez, Erik; Johnson, Amber; Boulgakov, Alexander; Bachman, Logan; Seifert, Helen. '''Improved single molecule sequencing'''. [https://patents.google.com/patent/US11162952B2/ 11,162,952 B2], issued November 2, 2021. [https://patents.google.com/patent/CA2961493C/en?oq=2%2c961%2c493 Canadian patent 2,961,493] issued October 3, 2023.</li>
<li value="10">  [https://patents.google.com/patent/US9625469 9,625,469], issued April, 18, 2017. '''Identifying peptides at the single molecule level'''. Marcotte, Edward; Swaminathan, Jagannath; Ellington, Andrew; Anslyn, Eric. Appl # 14128247, filed 22.06.2012; publication # US20140349860, 27.11.2014. [https://www.ipo.gov.uk/p-ipsum/Case/PublicationNumber/GB2510488 UK patent GB2510499] issued April 8, 2020. [https://patents.google.com/patent/US11105812B2 11,105,812 B2], issued August 31, 2021. [https://patents.google.com/patent/CA2839702C/en Canadian patent CA 2,839,702 C] issued April 20, 2021. [https://patents.google.com/patent/US11435358B2 US 11,435,358 B2], issued September 6, 2022. US application US 2023/0107647 A1 published April 6, 2023. [https://patents.google.com/patent/DE112012002570T5/en German patent DE 112012002570T5] issued August 10, 2023.</li>
<li value="9">  [https://patents.google.com/patent/WO2013067308A2 Publication # WO 2013067308 A2], '''Compositions and methods for inducing disruption of blood vasculature and for reducing angiogenesis''', PCT filed Nov 2, 2012; provisional patent # 61/555,212 filed Nov 3, 2011.</li>
<li value="8">  [https://patents.google.com/patent/WO2013055867A1 Publication # WO 2013055867 A1], '''Genes involved in stress response in plants''', PCT filed Oct 11, 2012.</li>
<li value="7">  [http://www.freshpatents.com/-dt20120823ptan20120215458.php USPTO Application # 20120215458], '''Orthologous phenotypes and non-obvious human disease models''', PCT filed July 13, 2010; provisional patent # 61/225,427 filed July 14, 2009.</li>
<li value="6">  [https://patents.google.com/patent/US9146241 9,146,241], issued September 29, 2015. '''Proteomic identification of antibodies'''. Lavinder, Jason; Wine, Yariv; Boutz, Danny; Marcotte, Edward; Georgiou, George. Appl # 13/684,395, filed November 23, 2012.</li>
<li value="5">  [https://patents.google.com/patent/US9090674B2 9,090,674 B2], issued July 28, 2015. '''Rapid isolation of monoclonal antibodies from animals'''. Reddy, Sai; Ge, Xin; Lavinder, Jason; Boutz, Danny; Ellington, Andrew D.; Marcotte, Edward M.; Georgiou, George. </li>
<li value="4">  [https://patents.google.com/patent/US6892139 6,892,139], issued May 10, 2005. '''Determining the functions and interactions of proteins by comparative analysis'''.</li>
<li value="3">  [https://patents.google.com/patent/US6772069 6,772,069], issued August 3, 2004. '''Determining protein function and interaction from genome analysis'''.</li>
<li value="2">  [https://patents.google.com/patent/US6564151 6,564,151], issued May 13, 2003. '''Assigning protein functions by comparative genome analysis protein phylogenetic profiles'''.</li>
<li value="1">  [https://patents.google.com/patent/US6466874 6,466,874], issued October 15, 2002. '''Rosetta stone method for detecting protein function and protein-protein interactions from genome sequences'''.
</li>
</li>
<li value="2"> {{Paper
|title=Control of cellular morphogenesis by the Ip12/Bem2 GTPase-activating protein: possible role of protein phosphorylation
|authors=Kim YJ, Francisco L, Chen GC, Marcotte E, Chan CS
|journal=J Cell Biol.
|pub_year=1994
|volume=127(5)
|page=1381-94
|pubmed=7962097
|link=http://jcb.rupress.org/cgi/reprint/127/5/1381
|pdf=JCellBiol_KimChan_Ipl2Bem2_1994.pdf
|comment=
}}
</li>
<li value="1"> {{Paper
|title=Crystallization of a chitosanase from <i>Streptomyces</i> N174
|authors=Marcotte E, Hart PJ, Boucher I, Brzezinski R, Robertus JD
|journal=J Mol Biol
|pub_year=1993
|volume=232(3)
|page=995-6
|pubmed=8355284
|link=http://dx.doi.org/10.1006/jmbi.1993.1447
|pdf=JMB_chitosanase_xtal_1993.pdf
|comment=
}}
</li>
</ol>
== Patents ==
<ol>
<li value="18"> [https://patents.google.com/patent/WO2021236716A2 Publication # WO 2021236716 A2] '''Methods, systems and kits for polypeptide processing and analysis'''. PCT filed May 19, 2021.
<li value="17"> [https://patents.google.com/patent/WO2021168083A1 Publication # WO 2021168083 A1] '''Peptide and protein c-terminus labeling'''. PCT filed Feb 18, 2021.
<li value="16"> [https://patents.google.com/patent/WO2020072907A1 Publication # WO 2020072907 A1] '''Solid-phase N-terminal peptide capture and release'''. PCT filed Oct 04, 2019.
<li value="15"> [https://patents.google.com/patent/WO2020037046A1 Publication # WO 2020037046 A1] '''Single molecule sequencing peptides bound to the major histocompatibility complex'''. PCT filed Aug 14, 2019. [https://patents.google.com/patent/GB2591384B/en UK patent GB 2591384 B] issued July 26, 2023. [https://patents.google.com/patent/GB2607829B/en UK patent GB 2607829 B] issued August 30, 2023.
<li value="14"> [https://patents.google.com/patent/WO2020023488A1/ Publication # WO 2020023488 A1] '''Single molecule sequencing identification of post-translational modifications on proteins'''. PCT filed July 23, 2018.
<li value="13"> [https://patents.google.com/patent/WO2020014586A1/ Publication # WO 2020014586 A1] '''Molecular neighborhood detection by oligonucleotides'''. PCT filed July 12, 2018.
<li value="12">  [https://patents.google.com/patent/US10175249B2 10,175,249 B2], issued January 8, 2019. '''Proteomic identification of antibodies'''. Lavinder, Jason; Boutz, Danny; Wine, Yariv; Marcotte, Edward; Georgiou, George. 
<li value="11">  [https://patents.google.com/patent/US10545153B2/ 10,545,153 B2], issued January 28, 2020. '''Single molecule peptide sequencing'''. [https://patentscope.wipo.int/search/en/detail.jsf?docId=WO2016069124 Publication # WO/2016/069124], Intl appl # PCT/US2015/050099, International filing date 15.09.2015. Marcotte, Edward; Anslyn, Eric; Ellington, Andrew;  Swaminathan, Jagannath; Hernandez, Erik; Johnson, Amber; Boulgakov, Alexander; Bachman, Logan; Seifert, Helen. '''Improved single molecule sequencing'''. [https://patents.google.com/patent/US11162952B2/ 11,162,952 B2], issued November 2, 2021. [https://patents.google.com/patent/CA2961493C/en?oq=2%2c961%2c493 Canadian patent 2,961,493] issued October 3, 2023.
<li value="10">  [https://patents.google.com/patent/US9625469 9,625,469], issued April, 18, 2017. '''Identifying peptides at the single molecule level'''. Marcotte, Edward; Swaminathan, Jagannath; Ellington, Andrew; Anslyn, Eric. Appl # 14128247, filed 22.06.2012; publication # US20140349860, 27.11.2014. [https://www.ipo.gov.uk/p-ipsum/Case/PublicationNumber/GB2510488 UK patent GB2510499] issued April 8, 2020. [https://patents.google.com/patent/US11105812B2 11,105,812 B2], issued August 31, 2021. [https://patents.google.com/patent/CA2839702C/en Canadian patent CA 2,839,702 C] issued April 20, 2021. [https://patents.google.com/patent/US11435358B2 US 11,435,358 B2], issued September 6, 2022. [https://patents.google.com/patent/DE112012002570T5/en German patent DE 112012002570T5] issued August 10, 2023.
<li value="9">  [https://patents.google.com/patent/WO2013067308A2 Publication # WO 2013067308 A2], '''Compositions and methods for inducing disruption of blood vasculature and for reducing angiogenesis''', PCT filed Nov 2, 2012; provisional patent # 61/555,212 filed Nov 3, 2011.</li>
<li value="8">  [https://patents.google.com/patent/WO2013055867A1 Publication # WO 2013055867 A1], '''Genes involved in stress response in plants''', PCT filed Oct 11, 2012.</li>
<li value="7">  [http://www.freshpatents.com/-dt20120823ptan20120215458.php USPTO Application # 20120215458], '''Orthologous phenotypes and non-obvious human disease models''', PCT filed July 13, 2010; provisional patent # 61/225,427 filed July 14, 2009.</li>
<li value="6">  [https://patents.google.com/patent/US9146241 9,146,241], issued September 29, 2015. '''Proteomic identification of antibodies'''. Lavinder, Jason; Wine, Yariv; Boutz, Danny; Marcotte, Edward; Georgiou, George. Appl # 13/684,395, filed November 23, 2012.
<li value="5">  [https://patents.google.com/patent/US9090674B2 9,090,674 B2], issued July 28, 2015. '''Rapid isolation of monoclonal antibodies from animals'''. Reddy, Sai; Ge, Xin; Lavinder, Jason; Boutz, Danny; Ellington, Andrew D.; Marcotte, Edward M.; Georgiou, George.
<li value="4">  [https://patents.google.com/patent/US6892139 6,892,139], issued May 10, 2005. '''Determining the functions and interactions of proteins by comparative analysis'''.</li>
<li value="3">  [https://patents.google.com/patent/US6772069 6,772,069], issued August 3, 2004. '''Determining protein function and interaction from genome analysis'''.</li>
<li value="2">  [https://patents.google.com/patent/US6564151 6,564,151], issued May 13, 2003. '''Assigning protein functions by comparative genome analysis protein phylogenetic profiles'''.</li>
<li value="1">  [https://patents.google.com/patent/US6466874 6,466,874], issued October 15, 2002. '''Rosetta stone method for detecting protein function and protein-protein interactions from genome sequences'''.</li>
</ol>
</ol>

Latest revision as of 03:27, 24 September 2025

2025

  1. McCafferty CL, Hoogerbrugge G, Papoulas O, Schwartz EA, Ritchey S, Taylor DW, Brilot AF, Marcotte EM, The CAGE complex: a hollow, megadalton, protein assembly in prokaryotic and eukaryotic microbes, bioRxiv, Sept 22: (2025) PubMed Link
  2. Papoulas O, Marcotte EM, Browning KS, Identification of Aspartyl-tRNA Synthetase as Co-purifying with Wheat Germ eIF2, MicroPubl Biol, Jul 9: (2025) PubMed Link
  3. Bai P, Vu MH, Komatsu C, Papoulas O, Ebine K, Nozawa A, Sawasaki T, Ueda T, Marcotte EM, Torii KU, Comparative Proteomic Profiling of Receptor Kinase Signaling Reveals Key Trafficking Components Enforcing Plant Stomatal Development, bioRxiv, Deposited July 23: (2025) PubMed Link
  4. Kipen J, Smith MB, Blom T, Zhou SB, Marcotte EM, Jaldén J, Protein Abundance Inference via Expectation Maximization in Fluorosequencing, bioRxiv, Deposited July 14: (2025) PubMed Link
  5. Reyes-Nava NG, Lee C, Papoulas O, Hong J, Marcotte EM, Wallingford JB, Physical and functional interaction of Lrrc56 and Odad3 controls deployment of axonemal dyneins in vertebrate multiciliated cells, bioRxiv, Deposited June 25: (2025) PubMed Link
  6. Dang V, Voigt B, Yang D, Hoogerbrugge G, Lee M, Cox RM, Papoulas O, McWhite CD, Pradeep R, Leggere JC, Gray RS, Marcotte EM, VerteBrain reveals novel neural and non-neural protein assemblies conserved across vertebrate evolution, bioRxiv, Deposited May 28: (2025) PubMed Link
  7. Vazquez N, Lee C, Valenzuela I, Phan TP, Derderian C, Chávez M, Mooney NA, Demeter J, Aziz-Zanjani MO, Cusco I, Codina M, Martínez-Gil N, Valverde D, Solarat C, Buel AL, Thauvin-Robinet C, Steichen E, Filges I, Joset P, De Geyter J, Vaidyanathan K, Gardner T, Toriyama M, Marcotte EM, Roberson EC, Jackson PK, Reiter JF, Tizzano EF, Wallingford JB, The human ciliopathy protein RSG1 links the CPLANE complex to transition zone architecture, Nature Communications, 16(1):5701 (2025) PubMed Link bioRxiv preprint (Deposited Sep 26, 2024)
  8. Maeda GP, Dang V, Kelly MK, Sundar A, Arnott R, Marcotte EM, Moran NA, Heritable symbiont producing nonribosomal peptide confers extreme heat sensitivity and antifungal protection on its host, Proc Natl Acad Sci U S A, 122(26):e2509873122 (2025) PubMed Link
  9. Gonzalez-Magaldi M, Gullapalli A, Papoulas O, Liu C, Leung AY-H, Guo L, Brilot A, Marcotte EM, Ke Z, Leahy DJ, Structure and organization of full-length Epidermal Growth Factor Receptor in extracellular vesicles by cryo-electron tomography, Proc Natl Acad Sci U S A, 122(23):e2424678122 (2025) PubMed Link bioRxiv preprint (Deposited Nov 28, 2024)
  10. Clark-ElSayed A, Ellington AD, Marcotte EM, Moving towards sequencing-based metabolomics, Trends in Genetics, 41(7):554-555 (2025) PubMed Link
  11. Acosta DJ, Barth DR, Bondy J, Appler KE, De Anda V, Ngo PHT, Alper HS, Baker BJ, Marcotte EM, Ellington AD, Plastic degradation by enzymes from uncultured deep sea microorganisms, ISME Journal, : (2025) PubMed
  12. Deol H, Raeisbahrami A, Ngo PHT, Swaminathan J, Papoulas O, Marcotte EM, Anslyn EV, After 75 Years, an Alternative to Edman Degradation: A Mechanistic and Efficiency Study of a Base-Induced Method for N‑Terminal Peptide Sequencing, Journal of the American Chemical Society, 147(16):13973-13982 (2025) PubMed Link
  13. Hoogerbrugge G, Keatinge-Clay AT, Marcotte EM, Serendipity and the slime mold: a visual survey of megadalton protein assemblies reveals the structure of the polyketide synthase Pks16, bioRxiv, Deposited Mar 12: (2025) PubMed Link
  14. Hong J, Lee C, Madhu G, Papoulas O, Atayeter E, Hoogerbrugge G, Pan J, Takagishi M, Manzi N, Dickinson DJ, Horani A, Brody SL, Marcotte EM, Prakash VN, Park TJ, Wallingford JB, A protein complex in the extreme distal tip of vertebrate motile cilia controls their organization, length, and function, bioRxiv, Deposited Feb 19: (2025) PubMed Link
  15. Dang V, Voigt B, Marcotte EM, Progress toward a comprehensive brain protein interactome, Biochemical Society Transactions, 53(1):303–314 (2025) PubMed Link PDF
  16. Panina SB, Irani S, Hardtke HA, Stephenson R, Floyd BM, Moreno RY, Marcotte EM, Zhang Q, Zhang YJ, Combinatorial phosphorylation on CTD of RNA polymerase II selectively controls transcription and export of protein-coding mRNAs, bioRxiv, Deposited Jan 15: (2025) PubMed Link

2024

  1. Moreno RY, Panina SB, Irani S, Hardtke HA, Richardson R, Floyd BM, Marcotte EM, Zhang Q, Zhang YJ, Thr4 phosphorylation on RNA Pol II occurs at early transcription regulating 3'-end processing, Science Advances, 10(36):eadq0350 (2024) PubMed Link PDF
  2. McWhite CD, Sae-Lee W, Yuan Y, Mallam AL, Gort-Frietas NA, Ramundo S, Onishi M, Marcotte EM, Alternative proteoforms and proteoform-dependent assemblies in humans and plants, Molecular Systems Biology, 20:933-951 (2024) PubMed Link PDF bioRxiv preprint (Deposited Sept 22, 2022)
  3. Cox RM, Papoulas O, Shril S, Lee C, Gardner T, Battenhouse AM, Lee M, Drew K, McWhite CD, Yang D, Leggere JC, Durand D, Hildebrandt F, Wallingford JB, Marcotte EM, Ancient eukaryotic protein interactions illuminate modern genetic traits and disorders, bioRxiv, Deposited May 29: (2024) PubMed Link
  4. McCafferty CL, Papoulas O, Lee C, Bui KH, Taylor DW, Marcotte EM, Wallingford JB, An amino acid-resolution interactome for motile cilia illuminates the structure and function of ciliopathy protein complexes, Developmental Cell, 60:1–14 (2025 (online 2024)) PubMed PDF bioRxiv preprint (deposited July 10, 2023)
  5. Smith MB, VanderVelden K, Blom T, Stout HD, Mapes JH, Folsom TM, Martin C, Bardo AM, Marcotte EM, Estimating error rates for single-molecule protein sequencing experiments, PLoS Computational Biology, 20(7):e1012258 (2024) PubMed Link bioRxiv preprint (deposited July 19, 2023)
  6. Mulvihill CJ, Lutgens J, Gollihar JD, Bachanová P, Tramont C, Marcotte EM, Ellington AD, Gardner EC, A Humanized CB1R Yeast Biosensor Enables Facile Screening of Cannabinoid Compounds, International Journal of Molecular Sciences, 25(11):6060 (2024) PubMed Link PDF bioRxiv preprint
  7. Kosonocky CW, Wilke CO, Marcotte EM, Ellington AD, Mining Patents with Large Language Models Demonstrates Congruence of Functional Labels and Chemical Structures, Digital Discovery, 3(6):1150-1159 (2024) PubMed Link PDF arXiv preprint (deposited Sept 15, 2023)
  8. Lee M, Guo Q, Kim M, Choi J, Segura A, Genceroglu A, LeBlanc L, Ramirez N, Jang YJ, Jang Y, Lee BK, Marcotte EM, Kim J, Systematic mapping of TF-mediated cell fate changes by a pooled induction coupled with scRNA-seq and multi-omics approaches, Genome Research, 34:1–14 (2024) PubMed Link PDF
  9. Orengo C, Ehrenreich IM, Marcotte EM, Kolodny R, Ben-Tal N, de Boer CG, McWhite CD, Ranganathan R, Honig B, Bromberg Y, Thornton JW, What can recent methodological advances help us understand about protein and genome evolution?, Cell Systems, 15(3):205-210 (2024) PubMed Link PDF
  10. Palukuri MV, Marcotte EM, DeepSLICEM: Clustering CryoEM particles using deep image and similarity graph representations, bioRxiv, Deposited Feb 8: (2024) PubMed Link
  11. Leggere J, Hibbard J, Papoulas O, Lee C, Pearson CG, Marcotte EM, Wallingford JB, Label-free proteomic comparison reveals ciliary and non- ciliary phenotypes of IFT-A mutants, Molecular Biology of the Cell, 35(ar39):1-14 (2024) PubMed Link PDF bioRxiv preprint (deposited Mar 9, 2023)

2023

  1. Goike J, Hsieh CL, Horton AP, Gardner EC, Zhou L, Bartzoka F, Wang N, Javanmardi K, Herbert A, Abbassi S, Xie X, Xia H, Shi PY, Renberg R, Segall-Shapiro TH, Terrace CI, Wu W, Shroff R, Byrom M, Ellington AD, Marcotte EM, Musser JM, Kuchipudi SV, Kapur V, Georgiou G, Weaver SC, Dye JM, Boutz DR, McLellan JS, Gollihar JD, SARS-COV-2 Omicron variants conformationally escape a rare quaternary antibody binding mode, Communications Biology, 6(1):1250 (2023) PubMed Link PDF
  2. Mapes JH, Stover J, Stout HD, Folsom TM, Babcock E, Loudwig S, Martin C, Austin MJ, Tu F, Howdieshell CJ, Simpson ZB, Blom T, Weaver D, Winkler D, Vander Velden K, Ossareh PM, Beierle JM, Somekh T, Bardo AM, Anslyn EV, Marcotte EM, Swaminathan J, Robust and scalable single-molecule protein sequencing with fluorosequencing, bioRxiv, Deposited Sept 16: (2023) PubMed Link
  3. Garge RK, Geck RC, Armstrong JO, Dunn B, Boutz DR, Battenhouse A, Leutert M, Dang V, Jiang P, Kwiatkowski D, Peiser T, McElroy H, Marcotte EM, Dunham MJ, Systematic Profiling of Ale Yeast Protein Dynamics across Fermentation and Repitching, G3, 14(3):jkad293 (2023) PubMed Link PDF bioRxiv preprint (deposited Sept 22, 2023)
  4. Ghanaeian A, Majhi S, McCafferty CL, Nami B, Black CS, Yang SK, Legal T, Papoulas O, Janowska M, Valente-Paterno M, Marcotte EM, Wloga D, Bui KH, Integrated modeling of the Nexin-dynein regulatory complex reveals its regulatory mechanism, Nature Communications, 14:5741 (2023) PubMed Link PDF bioRxiv preprint (deposited June 01, 2023)
  5. Moreno RY, Juetten KJ, Panina SB, Butalewicz JP, Floyd BM, Ramani MKV, Marcotte EM, Brodbelt JS, Zhang YJ, Distinctive interactomes of RNA polymerase II phosphorylation during different stages of transcription, iScience, 26(9):107581 (2023) PubMed Link PDF SSRN preprint (deposited May 17, 2023)
  6. Kubo S, Black CS, Joachimiak E, Yang SK, Legal T, Peri K, Khalifa AAZ, Ghanaeian A, McCafferty CL, Valente-Paterno M, De Bellis C, Huynh PM, Fan Z, Marcotte EM, Wloga D, Bui KH, Native doublet microtubules from Tetrahymena thermophila reveal the importance of outer junction proteins, Nature Communications, 14:Article number: 2168 (2023) PubMed Link PDF
  7. McCafferty CL, Pennington EL, Papoulas O, Taylor DW, Marcotte EM, Does AlphaFold2 model proteins' intracellular conformations? An experimental test using cross-linking mass spectrometry of endogenous ciliary proteins, Communications Biology, 6:Article number: 421 (2023) PubMed Link PDF bioRxiv preprint (deposited Aug 26, 2022)
  8. June V, Xu D, Papoulas O, Boutz D, Marcotte EM, Chen ZJ, Protein nonadditive expression and solubility contribute to heterosis in Arabidopsis hybrids and allotetraploids, Frontiers in Plant Science, 14:1252564 (2023) PubMed Link PDF bioRxiv preprint (deposited Mar 2, 2023)

2022

  1. Mulvihill CJ, Lutgens J, Gollihar JD, Bachanová P, Marcotte EM, Ellington AD, Gardner EC, Humanized CB1R and CB2R yeast biosensors enable facile screening of cannabinoid compounds, bioRxiv, Deposited Oct 12: (2022) PubMed Link
  2. Smith MB, Simpson ZB, Marcotte EM, Amino acid sequence assignment from single molecule peptide sequencing data using a two-stage classifier, PLoS Computational Biology, 19(5):e1011157 (2023) PubMed Link PDF bioRxiv preprint (deposited Sept 26, 2022)
  3. Sae-Lee W, McCafferty CL, Verbeke EJ, Havugimana PC, Papoulas O, McWhite CD, Houser JR, Vanuytsel K, Murphy G, Drew K, Emili A, Taylor DW, Marcotte EM, The protein organization of a red blood cell, Cell Reports, 40(3):111103 (2022) PubMed Link PDF bioRxiv preprint (deposited Dec 11, 2021)
  4. McCafferty CL, Papoulas O, Jordan MA, Hoogerbrugge G, Nichols C, Pigino G, Taylor DW, Wallingford JB, Marcotte EM, Integrative modeling reveals the molecular architecture of the Intraflagellar Transport A (IFT-A) complex, eLife, 11:e81977 (2022) PubMed Link PDF bioRxiv preprint (deposited Jul 5, 2022)
  5. Abdullah M, Greco BM, Laurent JM, Garge RK, Boutz DR, Vandeloo M, Marcotte EM, Kachroo AH, Rapid, scalable, combinatorial genome engineering by Marker-less Enrichment and Recombination of Genetically Engineered loci (MERGE), Cell Reports Methods, 3:100464 (2023) PubMed Link PDF bioRxiv preprint (deposited Jun 21, 2022) Supplement
  6. Palukuri MV, Patil RS, Marcotte EM, Molecular complex detection in protein interaction networks through reinforcement learning, BMC Bioinformatics, 24:306 (2023) PubMed Link bioRxiv preprint (deposited Jun 21, 2022) pdf available here
  7. Bachman JL, Wight CD, Bardo AM, Johnson AM, Pavlich CI, Boley AJ, Wagner HR, Swaminathan J, Iverson BL, Marcotte EM, Anslyn EV, Evaluating the Effect of Dye–Dye Interactions of Xanthene-Based Fluorophores in the Fluorosequencing of Peptides, Bioconjugate Chemistry, 33(6):1156-1165 (2022) PubMed Link PDF
  8. Kustatscher G, Collins T, Gingras AC, Guo T, Hermjakob H, Ideker T, Lilley KS, Lundberg E, Marcotte EM, Ralser M, Rappsilber R, An invitation to help define the challenge and goals for an understudied proteins initiative, Nature Biotechnology, 40(6):815-817 (2022) PubMed Link PDF
  9. Huebner RJ, Weng S, Lee C, Sarıkaya S, Papoulas O, Cox RM, Marcotte EM, Wallingford JB, ARVCF catenin controls force production during vertebrate convergent extension, Developmental Cell, 57:1-13 (2022) PubMed Link PDF bioRxiv preprint (deposited June 22, 2021, under the title Cell adhesions link subcellular actomyosin dynamics to tissue scale force production during vertebrate convergent extension)
  10. Kustatscher G, Collins T, Gingras AC, Guo T, Hermjakob H, Ideker T, Lilley KS, Lundberg E, Marcotte EM, Ralser M, Rappsilber R, Understudied proteins: Opportunities and challenges for functional proteomics, Nature Methods, 19:774–779 (2022) PubMed Link PDF
  11. Floyd BM, Marcotte EM, Protein sequencing, one molecule at a time, Annual Review of Biophysics, 51:181-200 (2022) PubMed Link PDF Author's free reprint access link

2021

  1. Hinson CM, Bardo AM, Shannon CE, Rivera S, Swaminathan J, Marcotte EM, Anslyn EV, Studies of Surface Preparation for the Fluorosequencing of Peptides, Langmuir, 37(51):14856–14865 (2021) PubMed Link PDF
  2. Kim CY, Baek S, Cha J, Yang S, Kim E, Marcotte EM, Hart T, Lee I, HumanNet v3: an improved database of human gene networks for disease research, Nucleic Acids Res, Nov 8:gkab1048: (2021) PubMed Link PDF
  3. Zhang L, Floyd BM, Chilamari M, Mapes J, Swaminathan J, Bloom S, Marcotte EM, Anslyn EV, Photoredox-catalyzed decarboxylative C-terminal differentiation for bulk and single molecule proteomics, ACS Chem Biol, 16:2595−2603 (2021) PubMed Link PDF bioRxiv preprint (deposited July 9, 2021)
  4. Palukuri MV, Marcotte EM, Super.Complex: A supervised machine learning pipeline for molecular complex detection in protein-interaction networks, PLoS One, 16(12):e0262056 (2021) PubMed Link PDF bioRxiv preprint (deposited October 11, 2021)
  5. Garge RK, Cha HJ, Lee, C, Gollihar JD, Kachroo AH, Wallingford JB, Marcotte EM, Discovery of new vascular disrupting agents based on evolutionarily conserved drug action, pesticide resistance mutations, and humanized yeast, Genetics, 219(1):iyab101 (2021) PubMed Link PDF bioRxiv preprint (deposited Sept 15, 2020 under the title Antifungal benzimidazoles disrupt vasculature by targeting one of nine β-tubulins) Commentary
  6. Bean BDM, Mulvihill C, Garge RK, Boutz DR, Rousseau O, Floyd BM, Cheney W, Gardner EC, Ellington AD, Marcotte EM, Gollihar JD, Whiteway M, Martin VJJ, Functional expression of opioid receptors and other human GPCRs in yeast engineered to produce human sterols, Nature Communications, 13(1):2882 (2022) PubMed PDF bioRxiv preprint (deposited May 14, 2021)
  7. Alfaro J, Bohländer P, Dai M, Filius M, Howard CJ, van Kooten XF, Ohayon S, Pomorski A, Schmid S, Aksimentiev A, Anslyn EV, Bedran G, Chan C, Chinappi M, Coyaud E, Dekker C, Dittmar G, Drachman N, Eelkema R, Goodlett D, Hentz S, Kalathiya U, Kelleher NL, Kelly RT, Kelman Z, Kim SH, Kuster B, Rodriguez-Larrea D, Lindsey S, Maglia G, Marcotte EM, Marino JP, Masselon C, Mayer M, Samaras P, Sarthak K, Sepiashvili L, Stein D, Wanunu M, Wilhelm M, Yin P, Meller A, Joo C, The emerging landscape of single-molecule protein sequencing technologies, Nature Methods, 18(6):604-617 (2021) PubMed Link PDF
  8. Goike J, Hsieh C-L, Horton A, Gardner AC, Bartzoka F, Wang N, Javanmardi K, Herbert A, Abbassi S, Renberg R, Johanson MJ, Cardona JA, Segall-Shapiro T, Zhou L, Nissly RH, Gontu A, Byrom M, Maranhao AC, Battenhouse AM, Gejji V, Soto-Sierra L, Foster ER, Woodard SL, Nikolov ZL, Lavinder J, Voss WN, Annapareddy A, Ippolito GC, Ellington AD, Marcotte EM, Finkelstein IJ, Hughes RA, Musser JM, Kuchipudi SJ, Kapur V, Georgiou G, Dye JM, Boutz DR, McLellan JS, Gollihar JD, Synthetic repertoires derived from convalescent COVID-19 patients enable discovery of SARS-CoV-2 neutralizing antibodies and a novel quaternary binding modality, bioRxiv, Posted April 9: (2021) PubMed Link
  9. McWhite CD, Papoulas O, Drew K, Dang V, Leggere JC, Sae-Lee W, Marcotte EM, Co-fractionation/mass spectrometry to identify protein complexes, STAR Protocols, 2(1):100370 (2021) PubMed Link PDF
  10. Roberson E, Battenhouse A, Garge RK, Tran NK, Marcotte EM, Wallingford JB, Spatiotemporal transcriptional dynamics of the cycling mouse oviduct, Developmental Biology, 476 (2021):240–248 (2021) PubMed Link PDF bioRxiv preprint (deposited Jan 15, 2021)
  11. McCafferty CL, Taylor DW, Marcotte EM, Improving integrative 3D modeling into low- to medium- resolution EM structures with evolutionary couplings, Protein Science, 30:1006–1021 (2021) PubMed Link PDF bioRxiv preprint (deposited January 14, 2021)

2020

  1. Floyd BM, Drew K, Marcotte EM, Systematic Identification of Protein Phosphorylation-Mediated Interactions, J Proteome Research, 20(2):1359-1370 (2021) PubMed Link PDF bioRxiv preprint (deposited Sept 19, 2020)
  2. Drew K, Wallingford JB, Marcotte EM, hu.MAP 2.0: Integration of over 15,000 proteomic experiments builds a global compendium of human multiprotein assemblies, Molecular Systems Biology, 17:e10016 (2021) PubMed Link PDF bioRxiv preprint (deposited Sept 16, 2020)
  3. Devitt C, Lee C, Cox R, Papoulas O, Alvarado J, Marcotte EM, Wallingford JB, Twinfilin1 controls lamellipodial protrusive activity and actin turnover during vertebrate gastrulation, J Cell Science, 134(14):jcs254011 (2021) PubMed Link PDF bioRxiv preprint (deposited September 3, 2020) Research Highlight
  4. Boulgakov AA, Moor SR, Jo HH, Metola P, Joyce LA, Marcotte EM, Welch CJ, Anslyn EV, Next-Generation TLC: A Quantitative Platform for Parallel Spotting and Imaging, J Org Chem, 85(15):9447–9453 (2020) PubMed Link PDF
  5. Garge RK, Laurent JM, Kachroo AH, Marcotte EM, Systematic humanization of the yeast cytoskeleton discerns functionally replaceable from divergent human genes, Genetics, 215(4):1153-1169 (2020) PubMed PDF bioRxiv preprint (deposited December 17, 2019)
  6. Laurent J, Garge RK, Teufel AI, Wilke CO, Kachroo AH, Marcotte EM, Humanization of yeast genes with multiple human orthologs reveals principles of functional divergence between paralogs, PLoS Biology, 18(5):e3000627 (2020) PubMed Link PDF bioRxiv preprint (deposited June 13, 2019)
  7. Lee C, Cox RM, Papoulas O, Horani A, Drew K, Devitt CC, Brody SL, Marcotte EM, Wallingford JB, Functional partitioning of a liquid-like organelle during assembly of axonemal dyneins, eLife, 9:e58662 (2020) PubMed Link PDF bioRxiv preprint (deposited April 21, 2020)
  8. McWhite CD, Papoulas O, Drew K, Cox RM, June V, Dong OX, Kwon T, Wan C, Salmi ML, Roux, SJ Jr., Browning KS, Chen ZJ, Ronald PC, Marcotte EM, A pan-plant protein complex map reveals deep conservation and novel assemblies, Cell, 181(2):460-474.e14 (2020) PubMed Link PDF bioRxiv preprint (deposited October 24, 2019) plant.MAP supporting web site Protein elution profile data repository on Zenodo
  9. McCafferty C, Verbeke EJ, Marcotte EM, Taylor DW, Structural Biology in the Multi-Omics Era, Journal of Chemical Information and Modeling, 60(5):2424-2429 (2020) PubMed Link PDF
  10. Blank HM, Papoulas O, Maitra N, Garge RK, Kennedy BK, Schilling B, Marcotte EM, Polymenis M, Abundances of transcripts, proteins, and metabolites in the cell cycle of budding yeast reveals coordinate control of lipid metabolism, Molecular Biology of the Cell, 31:1061-1084 (2020) PubMed Link PDF bioRxiv preprint (deposited Dec 18, 2019)
  11. Drew K, Lee C, Cox RM, Dang V, Devitt CC, Papoulas O, Huizar RL, Marcotte EM, Wallingford JB, A systematic, label-free method for identifying RNA-associated proteins in vivo provides insights into vertebrate ciliary beating, Developmental Biology, 467(1-2):108-117 (2020) PubMed Link PDF bioRxiv preprint (deposited Feb 27, 2020)
  12. Liebeskind BJ, Young RL, Halling DB, Aldrich RW, Marcotte EM, Mapping functional protein neighborhoods in the mouse brain, bioRxiv, Posted January 27: (2020) PubMed Link
  13. Howard CJ, Floyd BM, Bardo AM, Swaminathan J, Marcotte EM, Anslyn EV, Solid-phase peptide capture and release for bulk and single-molecule proteomics, ACS Chemical Biology, 15(6):1401-1407 (2020) PubMed Link PDF Supplement bioRxiv preprint (deposited January 14, 2020)
  14. Verbeke E, Zhou Y, Horton AP, Mallam AL, Taylor DW, Marcotte EM, Separating distinct structures of multiple macromolecular assemblies from cryo-EM projections, Journal of Structural Biology, 209(1):107416 (2020) PubMed Link PDF SLICEM code on Github bioRxiv preprint (deposited Apr 20, 2019)
  15. Bachman JL, Pavlich CI, Boley AJ, Marcotte EM, Anslyn EV, Synthesis of Carboxy ATTO 647N Using Redox Cycling for Xanthone Access, Org Lett, 22(2):381-385 (2020) PubMed Link PDF

2019

  1. McCafferty CL, Marcotte EM, Taylor DW, Simplified geometric representations of protein structures identify complementary interaction interfaces, Proteins: Structure, Function, and Bioinformatics, 89(3):348-360 (2021) PubMed Link PDF bioRxiv preprint (deposited Dec 23, 2019)
  2. Kim JJ, Lee SY, Gong F, Battenhouse AM, Boutz DR, Bashyal A, Refvik ST, Chiang CM, Xhemalce B, Paull TT, Brodbelt JS, Marcotte EM, Miller KM, Systematic bromodomain protein screens identify homologous recombination and R-loop suppression pathways involved in genome integrity, Genes and Development, 33(23-24):1751-1774 (2019) PubMed Link PDF
  3. Mallam AL, Sae-Lee W, Schaub JM, Tu F, Battenhouse A, Jang YJ, Kim J, Finkelstein IJ, Marcotte EM, Drew K, Systematic discovery of endogenous human ribonucleoprotein complexes, Cell Reports, 29(5):P1351-1368.e5 (2019) PubMed Link PDF bioRxiv preprint (deposited Nov 27, 2018)
  4. Liebeskind B, Aldrich RW, Marcotte EM, Ancestral Reconstruction of Protein Interaction Networks, PLoS Computational Biology, 15(10):e1007396 (2019) PubMed Link PDF bioRxiv preprint (deposited September 9, 2018)
  5. Glover N, Dessimoz C, Ebersberger I, Forslund SK, Gabaldón T, Huerta-Cepas J, Martin MJ, Muffato M, Patricio M, Pereira C, Sousa da Silva A, Wang Y, Sonnhammer E, Thomas PD; Quest for Orthologs Consortium, Advances and Applications in the Quest for Orthologs., Mol Biol Evol, 36(10):2157-2164 (2019) PubMed Link PDF
  6. Boulgakov AA, Ellington AD, Marcotte EM, Bringing Microscopy-By-Sequencing into View, Trends in Biotechnology, 38(2):154-162 (available online 2019, published 2020) PubMed Link PDF

2018

  1. Gibeaux R, Acker R, Kitaoka M, Georgiou G, van Kruijsbergen I, Ford B, Marcotte EM, Nomura DK, Kwon T, Veenstra GJC, Heald R, Paternal chromosome loss and metabolic crisis contribute to hybrid inviability in Xenopus, Nature, 553:337–341 (2018) PubMed Link PDF
  2. Huizar RL, Lee C, Boulgakov AA, Horani A, Tu F, Marcotte EM, Brody SL, Wallingford JB, A liquid-like organelle at the root of motile ciliopathy, eLife, 7:e38497 (2018) PubMed Link PDF bioRxiv preprint (deposited Nov 3, 2017)
  3. Boulgakov AA, Xiong E, Bhadra S, Ellington AD, Marcotte EM, From Space to Sequence and Back Again: Iterative DNA Proximity Ligation and its Applications to DNA-Based Imaging, bioRxiv, posted November 14: (2018) PubMed Link
  4. Hwang S, Kim CY, Yang S, Kim E, Hart T, Marcotte EM, Lee I, HumanNet v2: human gene networks for disease research, Nucleic Acids Res, 47 (D1):D573–D580 (2018,2019) PubMed Link PDF
  5. Swaminathan J, Boulgakov AA, Hernandez ET, Bardo AM, Bachman JL, Marotta J, Johnson AM, Anslyn EV, Marcotte EM, Highly parallel single-molecule identification of proteins in zeptomole-scale mixtures, Nature Biotechnology, 36:1076–1082 (2018) PubMed Link PDF Free access authors' view-only version at NBT Supplement Supplementary Tables github with code Data repository (Zenodo) News & Views Commentary in Phys.org
  6. Teufel AI, Johnson MM, Laurent JM, Kachroo AH, Marcotte EM, Wilke CO, The many nuanced evolutionary consequences of duplicated genes, Mol Bio Evol, 36(2):304-314 (2018) PubMed Link PDF bioRxiv preprint (deposited July 10, 2018)
  7. Sun X, Boulgakov AA, Smith L, Metola P, Marcotte EM, Anslyn EV, Photography Coupled with Self-Propagating Chemical Cascades. The Differentiation and Quantitation of G and V Nerve Agent Mimics via Chromaticity, ACS Central Science, 4(7):854-861 (2018) PubMed Link PDF
  8. Verbeke EJ, Mallam AL, Drew K, Marcotte EM, Taylor DW, Classification of single particles from human cell extract reveals distinct structures, Cell Reports, (24)1:259–268.e3 (2018) PubMed Link PDF bioRxiv preprint (deposited January 14 , 2018)
  9. Akhmetov A, Laurent JM, Gollihar J, Gardner EC, Garge RK, Ellington AD, Kachroo AH, Marcotte EM, Single-step precision genome editing in yeast using CRISPR-Cas9, Bio-protocol, 8(6):e2765 (2018) PubMed Link PDF
  10. Tu F, Sedzinski J, Ma Y, Marcotte EM, Wallingford JB, Protein localization screening in vivo reveals novel regulators of multiciliated cell development and function, J Cell Sci, 131 (3):jcs206565 (2018) PubMed Link PDF

2017

  1. Hernandez ET, Swaminathan J, Marcotte EM , Anslyn EV, Solution-phase and solid-phase sequential, selective modification of side chains in KDYWEC and KDYWE as models for usage in single-molecule protein sequencing, New Journal of Chemistry, 41:462-469 (2017) PubMed Link PDF
  2. Drew K, Müller CL, Bonneau R, Marcotte EM, Identifying direct contacts between protein complex subunits from their conditional dependence in proteomics datasets, PLoS Computational Biology, 13(10):e1005625 (2017) PubMed Link PDF
  3. Kuboniwa M, Houser JR, Hendrickson EL, Wang Q, Alghamdi SA, Sakanaka A, Miller DP, Hutcherson JA, Wang T, Beck DAC, Whiteley M, Amano A, Wang H, Marcotte EM, Hackett M, Lamont RJ, Metabolic crosstalk regulates Porphyromonas gingivalis colonization and virulence during oral polymicrobial infection, Nature Microbiology, 2:1493–1499 (2017) PubMed Link PDF
  4. Kachroo AH, Laurent JM, Akhmetov A, Szilagyi-Jones M, McWhite CD, Zhao A, Marcotte EM, Systematic bacterialization of yeast genes identifies a near-universally swappable pathway, eLife, 6:e25093 (2017) PubMed Link PDF
  5. Akhmetov A, Ellington A, Marcotte E, A highly parallel strategy for storage of digital information in living cells, BMC Biotechnology, 18:64 (2018) PubMed Link PDF bioRxiv preprint (deposited December 26, 2016) Open access pdf version of the article
  6. Mallam A, Marcotte EM, Systems-wide studies uncover Commander, a multiprotein complex essential to human development, Cell Systems, 4:483-494 (2017) PubMed Link PDF
  7. Drew, K., Lee, C., Huizar, R. L., Tu, F., Borgeson, B., McWhite, C. D., Ma, Y., Wallingford, J. B., Marcotte, E. M., Integration of over 9,000 mass spectrometry experiments builds a global map of human protein complexes, Molecular Systems Biology, 13:932 (2017) PubMed Link PDF bioRxiv preprint (deposited December 7, 2016)
  8. Shim JE, Bang C, Yang S, Lee T, Hwang S, Kim CY, Singh-Blom UM, Marcotte EM, Lee I, GWAB: a web server for the network-based boosting of human genome-wide association data, Nucleic Acids Research, 89(6):3747–3753 (2017) PubMed Link PDF
  9. Caglar MU, Houser JR, Barnhart CS, Boutz DR, Carroll SM, Dasgupta A, Lenoir WF, Smith BL, Sridhara V, Sydykova DK, Vander Wood D, Marx CJ, Marcotte EM, Barrick JE, Wilke CO, The E. coli molecular phenotype under different growth conditions, Scientific Reports, 7:45303 (2017) PubMed Link PDF
  10. Brown CW, Sridhara V, Boutz DR, Person MD, Marcotte EM, Barrick JE, Wilke CO, Large-scale analysis of post-translational modifications in E. coli under glucose-limiting conditions, BMC Genomics, 18(1):301 (2017) PubMed Link PDF
  11. AP Horton, SA Robotham, JR Cannon, DD Holden, EM Marcotte, Brodbelt JS, Comprehensive de novo peptide sequencing from MS/MS pairs generated through complementary collision induced dissociation and 351 nm ultraviolet photodissociation, Analytical Chemistry, 89(6):3747–3753 (2017) PubMed Link PDF
  12. Lee T, Hwang S, Kim CY, Shim H, Kim H, Ronald PC, Marcotte EM, Lee I, WheatNet: A genome-scale functional network for hexaploid bread wheat, Triticum aestivum, Molecular Plant, S1674-2052(17):30108-9 (2017) PubMed Link PDF bioRxiv preprint (deposited February 6, 2017)
  13. Hilterbrand AT, Boutz DR, Marcotte EM, Upton JW, Murine Cytomegalovirus Deubiquitinase Regulates Viral Chemokine Levels To Control Inflammation and Pathogenesis, mBio, 8:e01864-16 (2017) PubMed Link PDF

2016

  1. Young JH, Peyton M, Kim HS, McMillan E, Minna JD, White MA, Marcotte EM, Computational Discovery of Pathway-Level Genetic Vulnerabilities in Non-Small-Cell Lung Cancer, Bioinformatics, 32(9):1373-9 (2016) PubMed Link PDF Supporting code
  2. Lee J, Boutz DR, Chromikova V, Joyce MG, Vollmers C, Leung K, Horton AP, DeKosky BJ, Lee CH, Lavinder JJ, Murrin EM, Chrysostomou C, Hoi KH, Tsybovsky Y, Thomas PV, Druz A, Zhang B, Zhang Y, Wang L, Kong WP, Park D, Popova LI, Dekker CL, Davis MM, Carter CE, Ross TM, Ellington AD, Wilson PC, Marcotte EM, Mascola JR, Ippolito GC, Krammer F, Quake SR, Kwong PD, Georgiou G, Molecular-level analysis of the serum antibody repertoire in young adults before and after seasonal influenza vaccination, Nature Medicine, 22(12):1456-1464 (2016) PubMed Link PDF
  3. Session AM*, Uno Y*, Kwon T*, et al., Genome evolution in the allotetraploid frog Xenopus laevis, Nature, 538:336–343 (2016) PubMed Link PDF News&Views and pdf; Supplementary Information
  4. Wu GC, Cheung NV, Georgiou G, Marcotte EM, Ippolito GC, Temporal Stability and Molecular Persistence of the Bone Marrow Plasma Cell Antibody Repertoire, Nature Communications, 7:13838 (2016) PubMed Link PDF bioRxiv preprint (deposited August 2, 2016)
  5. Toriyama M, Lee C, Taylor SP, Duran I, Cohn DH, Bruel AL, Tabler JM, Drew K, Kelly MR, Kim S, Park TJ, Braun D, Pierquin G, Biver A, Wagner K, Malfroot A, Panigrahi I, Franco B, Al-Lami HA, Yeung Y, Choi YJ; University of Washington Center for Mendelian Genomics, Duffourd Y, Faivre L, Rivière JB, Chen J, Liu KJ, Marcotte EM, Hildebrandt F, Thauvin-Robinet C, Krakow D, Jackson PK, Wallingford JB, The ciliopathy-associated CPLANE proteins direct basal body recruitment of intraflagellar transport machinery, Nature Genetics, 48(6):648-56 (2016) PubMed Link PDF
  6. Young JH, Marcotte EM, Predicting Drug Synergy and Antagonism from Genetic Interaction Neighborhoods, bioRxiv, :deposited April 27 (2016) PubMed Link
  7. Young JH, Marcotte EM, Predictability of Genetic Interactions from Functional Gene Modules, G3, 7:617-624 (2016) PubMed Link PDF bioRxiv preprint (deposited April 25, 2016)
  8. Teperek M, Simeone A, Gaggioli V, Miyamoto K, Allen G, Erkek S, Peters A, Kwon T, Marcotte E, Zegerman P, Bradshaw C, Gurdon J, Jullien J, Sperm is epigenetically programmed to regulate gene transcription in embryos, Genome Research, 26:1034-1046 (2016) PubMed Link PDF
  9. Liebeskind BJ, McWhite CD, Marcotte EM, Towards Consensus Gene Ages, Genome Biology and Evolution, 8(6):1812-23 (2016) PubMed Link PDF bioRxiv preprint (deposited March 1) Supporting code and datasets
  10. Robotham SA, Horton AP, Cannon JR, Cotham VC, Marcotte EM, Brodbelt JS, UVnovo: A de Novo Sequencing Algorithm Using Single Series of Fragment Ions via Chromophore Tagging and 351 nm Ultraviolet Photodissociation Mass Spectrometry, Analytical Chemistry, 88(7):3990-7 (2016) PubMed Link PDF Supporting code

2015

  1. Woods JO, Tien M, Marcotte EM, Interrogating conserved elements of diseases using Boolean combinations of orthologous phenotypes, bioRxiv, posted April 13: (2015) PubMed Link
  2. Phanse S, Wan C, Borgeson B, Tu F, Drew K, Clark G, Xiong X, Kagan O, Kwan J, Bezginov A, Chessman K, Pal S, Cromar G, Papoulas O, Ni Z, Boutz DR, Stoilova S, Havugimana PC, Guo X, Malty RH, Sarov M, Greenblatt J, Babu M, Derry WB, R Tillier E, Wallingford JB, Parkinson J, Marcotte EM, Emili A, Proteome-wide dataset supporting the study of ancient metazoan macromolecular complexes, Data in Brief, 6:715-21 (2015) PubMed Link PDF
  3. Kim E, Hwang S, Kim H, Shim H, Kang B, Yang S, Shim JH, Shin SY, Marcotte EM, Lee I, MouseNet v2: A database of gene networks for studying the laboratory mouse and eight other model vertebrates, Nucl. Acid. Res., 44(D1):D848-54 (2015) PubMed Link PDF
  4. Murray J, Kwon T, Marcotte EM, Whiteley M, Intrinsic antimicrobial resistance determinants in the 'superbug' P. aeruginosa, mBio, 6(6):e01603-15 (2015) PubMed Link PDF
  5. Poldrack RA, Laumann T, Koyejo O, Gregory B, Hover A, Chen M-Y, Luci J, Huk A, Joo S-J, Boyd R, Hunicke-Smith S, Simpson ZB, Caven T, Sochat V, Shine JM, Gordon E, Snyder AZ, Adeyemo B, Petersen SE, Glahn D, Mckay DR, Blangero J, Frick L, Marcotte EM, Mumford JA, Long-term neural and physiological phenotyping of a single human, Nature Communications, 6:Article #8885 (2015) PubMed Link PDF
  6. Hwang S, Eiru K, Lee I, Marcotte EM, Systematic comparison of variant calling pipelines using gold standard personal exome variants, Scientific Reports, 5:17875 (2015) PubMed Link PDF Example variant calling parameters Gold standard vcf and exome capture region bed files
  7. Laurent JM, Young JH, Kachroo AH, Marcotte EM, Efforts to make and apply humanized yeast, Briefings in Functional Genomics, 15(2):155-63 (2015) PubMed Link PDF
  8. Wan C, Borgeson B, Phanse S, Tu F, Drew K, Clark G, Xiong X, Kagan O, Kwan J, Bezginov A, Chessman K, Pal S, Cromar G, Papoulas O, Ni Z, Boutz DR, Stoilova S, Havugimana PC, Guo X, Malty RH, Sarov M, Greenblatt J, Babu M, Derry WB, R Tillier E, Wallingford JB, Parkinson J, Marcotte EM, Emili A, Panorama of ancient metazoan macromolecular complexes, Nature, 525:339–344 (2015) PubMed Link PDF Supplementary data is available here. Supporting web site
  9. McWhite CD, Liebeskind BJ, Marcotte EM, Applications of comparative evolution to human disease genetics, Current Opinion in Genetics & Development, 35:16–24 (2015) PubMed Link PDF COGD supplies a direct link around their paywall for free access to the paper
  10. Houser JR, Barnhart C, Boutz DR, Carroll SM, Dasgupta A, Michener JK, Needham BD, Papoulas O, Sridhara V, Sydykova DK, Marx CJ, Trent MS, Barrick JE, Marcotte EM, Wilke CO, Controlled Measurement and Comparative Analysis of Cellular Components in E. coli Reveals Broad Regulatory Changes in Response to Glucose Starvation, PLoS Computational Biology, 11(8):e1004400 (2015) PubMed Link PDF
  11. Kachroo AH, Laurent JM, Yellman CM, Meyer AG, Wilke CO, Marcotte EM, Systematic humanization of yeast genes reveals conserved functions and genetic modularity, Science, 348(6237):921-925 (2015) PubMed Link PDF Supplement Supplementary Tables and Files Science magazine supplies a direct link around their paywall for free access to the manuscript and pdf reprint. Code and data for protein interaction evolution simulations are here
  12. Lee I, Kim E, Marcotte EM, Modes of Interaction between Individuals Dominate the Topologies of Real World Networks, PLoS One, 10(3):e0121248 (2015) PubMed Link PDF
  13. Sardana R, Liu X, Granneman S, Zhu J, Gill M, Papoulas O, Marcotte EM, Tollervey D, Correll CC, Johnson AW, The DEAH-box helicase Dhr1 dissociates U3 from the pre-rRNA to promote folding the central pseudoknot, PLoS Biology, 13(2):e1002083 (2015) PubMed Link PDF
  14. Brown KA, Yang X, Schipper D, Hall JW, DePue LJ, Gnanam AJ, Arambula JF, Jones JN, Swaminathan J, Dieye Y, Vadivelu J, Chandler DJ, Marcotte EM, Sessler JL, Ehrlich LIR, Jones RA, A self-assembling lanthanide molecular nanoparticle for optical imaging, Dalton Transactions, 44(6):2667-75 (2015) PubMed Link PDF

2014

  1. Swaminathan J, Boulgakov AA, Marcotte EM, A theoretical justification for single molecule peptide sequencing, PLoS Computational Biology, 11(2):e1004080 (2014 bioRxiv, 2015 PLoS CB) PubMed Link PDF bioRxiv preprint
  2. Jones RA, Gnanam AJ, Arambula JF, Jones JN, Swaminathan J, Yang X, Schipper D, Hall JW, DePue LJ, Dieye Y, Vadivelu J, Chandler DJ, Marcotte EM, Sessler JL, Ehrlich LIR, Brown KA, Lanthanide nano-drums: A new class of molecular nanoparticles for potential biomedical applications, Faraday Discussions, 175:241-55 (2014) PubMed Link PDF
  3. Kwon T, Chung M-I, Gupta R, Baker JC, Wallingford JB, Marcotte EM, Identifying direct targets of transcription factor Rfx2 that coordinate ciliogenesis and cell movement, Genomics Data, 2:192-194 (2014) PubMed Link PDF
  4. Hwang S, Kim E, Yang S, Marcotte EM, Lee I, MORPHIN: a web tool for human disease research by projecting model organism biology onto a human integrated gene network, Nucleic Acids Research, 42(Web Server issue):W147-53 (2014) PubMed Link PDF
  5. Kwon T, Huse HK, Vogel C, Whiteley M, Marcotte EM, Protein-to-mRNA ratios are conserved between Pseudomonas aeruginosa strains, Journal of Proteome Research, 13(5):2370-80 (2014) PubMed Link PDF
  6. Boutz DR, Horton AP, Wine Y, Lavinder JJ, Georgiou G, Marcotte EM, Proteomic identification of monoclonal antibodies from serum, Analytical Chemistry, 86(10):4758-66 (2014) PubMed Link PDF
  7. O’Connell JD, Tsechansky M, West-Driga M, Marcotte EM, Formation of intracellular glutamine synthetase bodies depends strongly upon cellular age and glucose availability, PeerJ PrePrints, 2:e270v1 (2014) PubMed Link PDF
  8. O’Connell JD, Tsechansky M, Royall A, Boutz DR, Ellington AD, Marcotte EM, A proteomic survey of widespread protein aggregation in yeast, Molecular BioSystems, 10:851-861 (2014) PubMed Link PDF Supplement Supporting Datasets
  9. Hammerling MJ, Ellefson JW, Boutz DR, Marcotte EM, Ellington AD, Barrick JE, Bacteriophages use an expanded genetic code on evolutionary paths to higher fitness, Nature Chemical Biology, 10(3):178-80 (2014) PubMed Link PDF Supplement Supplemental Data 1 Supplemental Data 2
  10. Qian Y, Kachroo A, Yellman CM, Marcotte EM, Johnson KA, Yeast cells expressing the human mitochondrial DNA polymerase reveal correlations between polymerase fidelity and human disease progression, Journal of Biological Chemistry, 289:5970-5985 (2014) PubMed Link PDF
  11. Lavinder JJ, Wine Y, Giesecke C, Ippolito GC, Horton AP, Lungu OI, Hoi KH, Dekosky BJ, Murrin EM, Wirth MM, Ellington AD, Dörner T, Marcotte EM, Boutz DR, Georgiou G, Identification and characterization of the constituent human serum antibodies elicited by vaccination, Proc Natl Acad Sci USA, 111(6):2259-64 (2014) PubMed Link PDF
  12. Zhao A, Tsechansky M, Ellington AD, Marcotte EM, Revisiting and revising the purinosome, Molecular BioSystems, 10(3):369-74 (2014) PubMed Link PDF
  13. Chung MI*, Kwon T*, Tu F, Brooks ER, Gupta R, Meyer M, Baker JC, Marcotte EM, Wallingford JB, Coordinated genomic control of ciliogenesis and cell movement by Rfx2, eLife, 3:e01439 (2014) PubMed Link PDF Supplement

2013

  1. Gerster S, Kwon T, Ludwig C, Matondo M, Vogel C, Marcotte E, Aebersold R, Bühlmann P, Statistical approach to protein quantification, Mol Cell Proteomics, 13(2):666-77 (2014) PubMed Link PDF
  2. Huse HK, Kwon T, Zlosnik JEA, Speert DP, Marcotte EM, Whiteley M, Pseudomonas aeruginosa enhances production of a non-alginate exopolysaccharide during long-term colonization of the cystic fibrosis lung, PLoS One, 8(12):e82621 (2013) PubMed Link PDF
  3. Li Z*, Park Y*, Marcotte EM, A bacteriophage tailspike domain promotes self-cleavage of a human membrane-bound transcription factor, the myelin regulatory factor MYRF, PLoS Biology, 11(8):e1001624 (2013) PubMed Link PDF Commentary
  4. Woods JO, Singh-Blom UM, Laurent JM, McGary KL, Marcotte EM, Prediction of gene-phenotype associations in humans, mice, and plants using phenologs, BMC Bioinformatics, 14:203 (2013) PubMed Link PDF
  5. Singh-Blom UM, Natarajan N, Tewari A, Woods JO, Dhillon IS, Marcotte EM, Prediction and validation of gene-disease associations using methods inspired by social network analyses, PLoS One, 8(5):e58977 (2013) PubMed Link PDF Supplement
  6. Zhou L, Zhang AB, Wang R, Marcotte EM, Vogel C, The proteomic response to mutants of the Escherichia coli RNA degradosome, Molecular BioSystems, 9:750-757 (2013) PubMed Link PDF
  7. Wine Y, Boutz DR, Lavinder JJ, Miklos AE, Hughes RA, Hoi KH, Jung ST, Horton AP, Murrin EM, Ellington AD, Marcotte EM, Georgiou G, Molecular deconvolution of the monoclonal antibodies that comprise the polyclonal serum response, Proc Natl Acad Sci USA, 110(8):2993–2998 (2013) PubMed Link PDF
  8. Zhao A, Tsechansky M, Swaminathan J, Cook L, Ellington AD, Marcotte EM, Transiently transfected purine biosynthetic enzymes form stress bodies, PLoS One, 8(2):e56203 (2013) PubMed Link PDF

2012

  1. Wang PI, Hwang S, Kincaid RP, Sullivan CS, Lee I, Marcotte EM, RIDDLE: Reflective diffusion and local extension reveal functional associations for unannotated gene sets via proximity in a gene network, Genome Biology, 13(12):R125 (2012) PubMed Link PDF
  2. Wessel AK, Liew J, Kwon T, Marcotte EM, Whiteley M, The role of Pseudomonas aeruginosa peptidoglycan-associated outer membrane proteins in vesicle formation, J Bacteriol, 195(2):213-9 (2012) PubMed Link PDF Supplemental data
  3. Park Y, Marcotte EM, Flaws in evaluation schemes for pair-input computational predictions, Nature Methods, 9(12):1134–1136 (2012) PubMed Link PDF Supplement
  4. Havugimana PC, Hart GT, Nepusz T, Yang H, Turinsky AL, Li Z, Wang P, Boutz DR, Fong V, Babu M, Craig SA, Hu P, Phanse S, Wan C, Vlasblom J, Dar V, Bezginov A, Wu GC, Wodak SJ, Tillier ERM, Paccanaro A, Marcotte EM, Emili A, Census of human soluble protein complexes, Cell, 150:1068-1081 (2012) PubMed Link PDF Supporting web site Research highlight
  5. Uribe RA, Kwon T, Marcotte EM, Gross JM, Id2a functions to limit Notch pathway activity and thereby influence retinoblast proliferation to differentiation of retinoblasts during zebrafish retinogenesis, Developmental Biology, 371:280–292 (2012) PubMed Link PDF
  6. Cha HJ, Byrom M, Mead PE, Ellington AD, Wallingford JB, Marcotte EM, Evolutionarily repurposed networks reveal the well-known antifungal drug thiabendazole to be a novel vascular disrupting agent, PLoS Biology, 10(8):e1001379 (2012) PubMed Link PDF Supplemental Material Synopsis NY Times NIGMS video
  7. O'Connell JD, Zhao A, Ellington AD, Marcotte EM, Dynamic reorganization of metabolic enzymes into intracellular bodies, Annual Review of Cell and Developmental Biology, 28:89-111 (2012) PubMed Link PDF
  8. Vogel C, Marcotte EM, Insights into the regulation of protein abundance from proteomic and transcriptomic analyses, Nature Reviews Genetics, 13:227-232 (2012) PubMed Link PDF
  9. Orr SJ, Boutz DR, Wang R, Chronis C, Lea NC, Thayaparan T, Hamilton E, Milewicz H, Blanc E, Mufti GJ, Marcotte EM, Thomas NSB, Proteomic and protein interaction network analysis of human T lymphocytes during cell-cycle entry, Molecular Systems Biology, 8:573 (2012) PubMed Link PDF Supplement Reviewer comments
  10. Chung M-I, Peyrot S, LeBoeuf S, Park TJ, McGary KL, Marcotte EM, Wallingford JB, RFX2 is broadly required for ciliogenesis during vertebrate development, Developmental Biology, 363(1):155-165 (2012) PubMed Link PDF Supplement
  11. Vogel C, Marcotte EM, Label-free quantitation using weighted spectral counting, Methods in Molecular Biology: Quantitative Methods in Proteomics, Marcus, K., ed., Humana Press, vol. 893(3):321-341 (2012) PubMed Link PDF

2011

  1. Lee I, Seo Y-S, Coltrane D, Hwang S, Oha T, Marcotte EM, Ronald PC, Genetic dissection of the biotic stress response using a genome-scale gene network for rice, Proc Natl Acad Sci USA, 108(45):18548-18553 (2011) PubMed Link PDF Supplement
  2. Natarajan N, Blom UM, Tewari A, Woods JO, Dhillon IS, Marcotte EM, Predicting gene-disease associations using multiple species data, UTCS Technical Report, TR-11-37: (2011) PubMed Link PDF
  3. Vogel C, Silva GM, Marcotte EM, Global protein expression regulation under oxidative stress, Molecular and Cellular Proteomics, 10(12):M111.009217 (2011) PubMed Link PDF Supplement
  4. Park Y, Marcotte EM, Revisiting the negative example sampling problem for predicting protein-protein interactions, Bioinformatics, 27(21):3024-3028 (2011) PubMed Link PDF Supplemental Data
  5. Hwang S, Rhee SY, Marcotte EM, Lee I, Systematic prediction of gene function using a probabilistic functional gene network for Arabidopsis thaliana, Nature Protocols, 6:1429–1442 (2011) PubMed Link PDF
  6. Lee I, Blom M, Wang PI, Shim JE, Marcotte EM, Prioritizing candidate disease genes by network-based boosting of genome-wide association data, Genome Research, 21(7):1109-21 (2011) PubMed Link PDF Supplement HumanNet web site
  7. Kwon T, Choi H, Vogel C, Nesvizhskii AI, Marcotte EM, MSblender: a probabilistic approach for integrating peptide identifications from multiple database search engines, Journal of Proteome Research, 10(7):2949-58 (2011) PubMed Link PDF Supplemental Figures 1 2 3 4 Supporting web site
  8. Boutz DR, Collins P, Suresh U, Lu M, Ramírez CM, Fernández-Hernando C, Huang Y, de Sousa Abreu R, Le SY, Shapiro BA, Liu AM, Luk JM, Aldred SF, Trinklein N, Marcotte EM, Penalva LO, A two-tiered approach identifies a network of cancer and liver diseases related genes regulated by miR-122, Journal of Biological Chemistry, 286(20):18066-78 (2011) PubMed Link PDF
  9. Niu W, Hart GT, Marcotte EM, High-throughput immunofluorescence microscopy using yeast spheroplast microarrays, Methods in Molecular Biology: Cell-Based Microarrays, Palmer, E., ed., Humana Press, vol. 706:83-95 (2011) PubMed PDF
  10. Smith KR, Kieserman EK, Wang PI, Basten SG, Giles RH, Marcotte EM, Wallingford JB, A role for central spindle proteins in cilia structure and function, Cytoskeleton, 68(2):112-24 (2011) PubMed Link PDF

2010

  1. Huse HK, Kwon T, Zlosnik JEA, Speert DP, Marcotte EM, Whiteley M, Parallel evolution in Pseudomonas aeruginosa over 39,000 generations in vivo, mBIO, 1(4):e00199-10 (2010) PubMed Link PDF ScienceNews Supplement
  2. Huang N, Lee I, Marcotte EM, Hurles M, Characterising and predicting haploinsufficiency in the human genome, PLoS Genetics, 6(10):e1001154 (2010) PubMed Link PDF
  3. Laurent J, Vogel C, Kwon T, Craig SA, Boutz DR, Huse HK, Nozue K, Walia H, Whiteley M, Ronald PC, Marcotte EM, Protein abundances are more conserved than mRNA abundances across diverse taxa, Proteomics, 10:4209–4212 (2010) PubMed Link PDF Supplement
  4. Wang PI, Marcotte EM, It's the machine that matters: predicting gene function and phenotype from protein networks, Journal of Proteomics, 73(11):2277-89 (2010) PubMed Link PDF
  5. Vogel C, de Sousa Abreu R, Ko D, Le S-Y, Shapiro BA, Burns SC, Sandhu D, Boutz DR, Marcotte EM, Penalva LO, Sequence signatures and mRNA concentration can explain two-thirds of protein abundance variation in a human cell line, Molecular Systems Biology, 6:article 400 (2010) PubMed Link PDF Supplement Supplemental Data (Excel format) Fig 2 source data Fig 3A source data Fig 3B source data News and Views
  6. Lo K-Y, Li Z, Bussiere C, Bresson S, Marcotte EM, Johnson AW, Defining the pathway of cytoplasmic maturation of the 60S ribosomal subunit, Molecular Cell, 39(2):196-208 (2010) PubMed Link PDF Supplement
  7. Lee I, Lehner B, Vavouri T, Shin J, Fraser AG, Marcotte EM, Predicting genetic modifier loci using functional gene networks, Genome Research, 20:1143-1153 (2010) PubMed Link PDF Supplement Nature Reviews Genetics
  8. McGary KL, Park TJ, Woods JO, Cha HJ, Wallingford JB, Marcotte EM, Systematic discovery of nonobvious human disease models through orthologous phenotypes, Proc Natl Acad Sci U S A, 107(14):6544-9 (2010) PubMed Link PDF Supplement Nature News The Scientist(blog) NY Times Genome Biology
  9. Orr SJ, Gaymes T, Ladon D, Chronis C, Czepulkowski B, Wang R, Mufti GJ, Marcotte EM, Thomas NSB, Reducing MCM levels in human primary T cells during the G0->G1 transition causes genomic instability during the first cell cycle, Oncogene, 29(26):3803-14 (2010) PubMed Link PDF
  10. Lee I, Ambaru B, Thakkar P, Marcotte EM, Rhee SY, Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana, Nature Biotechnology, 28(2):149-156 (2010) PubMed Link PDF Supplement Honorable Mention in the 2010 Science Visualization Challenge New York Times slideshow

2009

  1. Li Z, Lee I, Moradi E, Hung NJ, White J, Johnson AW, Marcotte EM, Rational extension of the ribosome biogenesis pathway using network-guided genetics, PLoS Biology, 7(10):e1000213 (2009) PubMed Link PDF Supplemental Figures and Tables
  2. Hart GT, Zhao A, Garg A, Bolusani S, Marcotte EM, Human cell chips: adapting DNA microarray spotting technology to cell-based imaging assays, PLoS One, 4(10):e7088 (2009) PubMed Link PDF Table S1
  3. Lo KY, Li Z, Wang F, Marcotte EM, Johnson AF, Ribosome stalk assembly requires the dual specificity phosphatase Yvh1 for the exchange of Mrt4 with P0, J. Cell Biology, 186(6):849-62 (2009) PubMed Link PDF Supplemental material
  4. Vogel C, Marcotte EM, Absolute abundance for the masses, Nature Biotechnology, 27(9):825-6 (2009) PubMed Link PDF
  5. de Sousa Abreu R, Penalva LO, Marcotte EM, Vogel C, Global signatures of protein and mRNA expression levels, Molecular BioSystems, 5:1512–1526 (2009) PubMed Link PDF
  6. Gray RS, Abitua PB, Wlodarczyk BJ, Blanchard O, Lee I, Weiss G, Marcotte EM, Wallingford JB, Finnell RH, The planar cell polarity effector protein Fuzzy is essential for targeted membrane trafficking, ciliogenesis, and mouse embryonic development, Nature Cell Biology, 11(10):1225-32 (2009) PubMed Link PDF Journal cover--a beautiful electron micrograph by Phil Abitua Supplemental Figures
  7. Marcotte EM, Tsechansky M, Disorder, promiscuity, and toxic partnerships, Cell, 138(1):16-18 (2009) PubMed Link PDF
  8. Ramakrishnan SR, Vogel C, Kwon T, Penalva LO, Marcotte EM, Miranker DP, Mining gene functional networks to improve mass-spectrometry based protein identification, Bioinformatics, 25(22):2955-2961 (2009) PubMed Link PDF Supplemental Website
  9. Narayanaswamy R, Levy M, Tsechansky M, Stovall GM, O'Connell J, Mirrielees J, Ellington AD, Marcotte EM, Widespread reorganization of metabolic enzymes into reversible assemblies upon nutrient starvation, Proc Natl Acad Sci U S A, 106(25):10147-52 (2009) PubMed Link PDF Supplemental methods Supplemental Dataset Table S1 Table S2 Table S3
  10. Tabor JJ, Salis H, Simpson ZB, Chevalier AA, Levskaya A, Marcotte EM, Voigt CA, Ellington AD, A synthetic genetic edge detection program, Cell, 137(7):1272-1281 (2009) PubMed Link PDF Supplemental methods
  11. Lee I, Marcotte EM, Effects of functional bias on supervised learning of a gene network model, Methods Mol Biol, 541:463-75 (2009) PubMed Link PDF
  12. Ramakrishnan SR, Vogel C, Prince JT, Wang R, Li Z, Penalva LO, Myers M, Marcotte EM, Miranker DP, Integrating shotgun proteomics and mRNA expression data to improve protein identification, Bioinformatics, 25(11):1397-403 (2009) PubMed Link PDF Supplement Supplemental website
  13. Narayanaswamy R, Moradi EK, Niu W, Hart GT, Davis M, McGary KL, Ellington AD, Marcotte EM., Systematic definition of protein constituents along the major polarization axis reveals an adaptive reuse of the polarization machinery in pheromone-treated budding yeast., J Proteome Res., 8(1):6-19. (2009) PubMed Link PDF

2008

  1. Hannay K, Marcotte EM, Vogel C, Buffering by gene duplicates: an analysis of molecular correlates and evolutionary conservation, BMC Genomics, 9:609 (2008) PubMed Link PDF Supplemental Notes Supplemental Data
  2. Braisted JC, Kuntumalla S, Vogel C, Marcotte EM, Rodrigues AR, Wang R, Huang ST, Ferlanti ES, Saeed AI, Fleischmann RD, Peterson SN, Pieper R, The APEX Quantitative Proteomics Tool: generating protein quantitation estimates from LC-MS/MS proteomics results, BMC Bioinformatics, 9:529. (2008) PubMed Link PDF
  3. Kim WK, Marcotte EM, Age-dependent evolution of the yeast protein interaction network suggests a limited role of gene duplication and divergence, PLoS Comput Biol, 4(11):e1000232 (2008) PubMed Link PDF Supporting python code: network_growth_functions_fixed_module.py Note that this code used an older version of the igraph library (0.4.2); the latest version that we've tested (0.5.2) gives somewhat fewer large clusters than our published clusters due to changes in the function "G.community_fastgreedy()", possibly resulting from modifications to the handling of ties in the community merging process. The previous igraph library (0.4.2) is linked here: python-igraph-0.4.2.tar.gz igraph-0.4.2.tar.gz igraph_base.py
  4. Prince JT, Marcotte EM, mspire: mass spectrometry proteomics in Ruby, Bioinformatics, 24(23):2796-7 (2008) PubMed Link PDF
  5. Vogel C, Marcotte EM, Calculating absolute and relative protein abundance from mass spectrometry-based protein expression data, Nat Protoc, 3(9):1444-51. (2008) PubMed Link PDF Supplement
  6. Lee I, Marcotte EM, Integrating functional genomics data, Methods Mol Biol, 453:267-78. (2008) PubMed Link PDF
  7. Kim WK, Krumpelman C, Marcotte EM, Inferring mouse gene functions from genomic-scale data using a combined functional network/classification strategy, Genome Biol, 9 Suppl 1::S5 (2008) PubMed Link PDF Supplement
  8. Peña-Castillo L, Tasan M, Myers CL, Lee H, Joshi T, Zhang C, Guan Y, Leone M, Pagnani A, Kim WK, Krumpelman C, Tian W, Obozinski G, Qi Y, Mostafavi S, Lin GN, Berriz GF, Gibbons FD, Lanckriet G, Qiu J, Grant C, Barutcuoglu Z, Hill DP, Warde-Farley D, Grouios C, Ray D, Blake JA, Deng M, Jordan MI, Noble WS, Morris Q, Klein-Seetharaman J, Bar-Joseph Z, Chen T, Sun F, Troyanskaya OG, Marcotte EM, Xu D, Hughes TR, Roth FP, A critical assessment of Mus musculus gene function prediction using integrated genomic evidence, Genome Biol, 9 Suppl 1:S2 (2008) PubMed Link PDF MouseFunc predictions
  9. Niu W, Li Z, Zhan W, Iyer VR, Marcotte EM, Mechanisms of cell cycle control revealed by a systematic and quantitative overexpression screen in S. cerevisiae, PLoS Genet, 4(7):e1000120 (2008) PubMed Link PDF Supplemental File of All ORF FACS Defects
  10. Zhao J, Niu W, Yao J, Mohr S, Marcotte EM, Lambowitz AM, Group II intron protein localization and insertion sites are affected by polyphosphate, PLoS Biol, 6(6):e150 (2008) PubMed Link PDF
  11. Ramani AK, Li Z, Hart GT, Carlson MW, Boutz DR, Marcotte EM, A map of human protein interactions derived from co-expression of human mRNAs and their orthologs, Mol Syst Biol, 4:180 (2008) PubMed Link PDF
  12. White J, Li Z, Sardana R, Bujnicki JM, Marcotte EM, Johnson AW, Bud23 methylates G1575 of 18S rRNA and is required for efficient nuclear export of pre-40S subunits, Mol Cell Biol, 28(10):3151-61 (2008) PubMed Link PDF
  13. Wang R, Marcotte EM, The proteomic response of Mycobacterium smegmatis to anti-tuberculosis drugs suggests targeted pathways, J Proteome Res, 7(3):855-65 (2008) PubMed Link PDF
  14. Lee I, Lehner B, Crombie C, Wong W, Fraser AG, Marcotte EM, A single gene network accurately predicts phenotypic effects of gene perturbation in Caenorhabditis elegans, Nat Genet, 40(2):181-8 (2008) PubMed Link PDF Supplement Supplemental Web Site

2007

  1. McGary KL, Lee I, Marcotte EM, Broad network-based predictability of Saccharomyces cerevisiae gene loss-of-function phenotypes, Genome Biol, 8(12):R258. (2007) PubMed Link PDF Supplemental Web Site
  2. Lee I, Li Z, Marcotte EM, An improved, bias-reduced probabilistic functional gene network of baker's yeast, Saccharomyces cerevisiae, PLoS ONE, 2(10):e988 (2007) PubMed Link PDF Supplemental Web Site
  3. Marcotte EM, How do shotgun proteomics algorithms identify proteins?, Nat Biotechnol, 25(7):755-7 (2007) PubMed Link PDF
  4. Carlson MW, Iyer VR, Marcotte EM, Quantitative gene expression assessment identifies appropriate cell line models for individual cervical cancer pathways, BMC Genomics, 8:117. (2007) PubMed Link PDF
  5. Lu P, Vogel C, Wang R, Yao X, Marcotte EM, Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation, Nat Biotechnol, 25(1):117-24 (2007) PubMed Link PDF Supplement Supplemental Data (zipped folder) News & Views 1 News & Views 2 News & Views 3 2011 NBT Retrospective on APEX
  6. Lu P, Rangan A, Chan SY, Appling DR, Hoffman DW, Marcotte EM, Global metabolic changes following loss of a feedback loop reveal dynamic steady states of the yeast metabolome, Metab Eng, 9(1):8-20 (2007) PubMed Link PDF Supplemental File 1 Supplemental File 2 Supplemental File 3
  7. Hart GT, Lee I, Marcotte EM, A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality, BMC Bioinformatics, 8:236. (2007) PubMed Link PDF

2006

  1. Hart GT, Ramani AK, Marcotte EM., How complete are current yeast and human protein-interaction networks?, Genome Biol., 7(11):120 (2006) PubMed Link PDF Additional Data File 1
  2. Prince JT, Marcotte EM, Chromatographic alignment of ESI-LC-MS proteomics datasets by ordered bijective interpolated warping, Anal. Chem., 78(17):6140-52 (2006) PubMed Link PDF
  3. Ramakrishnan SR, Mao R, Nakorchevskiy AA, Prince JT, Willard WS, Xu W, Marcotte EM, Miranker DP, A fast coarse filtering method for peptide identification by mass spectrometry, Bioinformatics, 22(12):1524-31 (2006) PubMed Link PDF
  4. Narayanaswamy R, Niu W, Scouras A, Hart GT, Davies J, Ellington AD, Iyer VR, Marcotte EM, Systematic profiling of cellular phenotypes with spotted cell microarrays reveals new pheromone response genes, Genome Biol., 7(1):R6 (2006) PubMed Link PDF Supplement Supplemental Table 1 Supplemental Table 2 Supplemental Table 3 Supplemental Table 4
  5. Lee I, Narayanaswamy R, Marcotte EM, Bioinformatic prediction of yeast gene function, Yeast Gene Analysis, Stansfield, I., ed., Elsevier Press: (2006) PubMed PDF
  6. Eisenberg D, Marcotte E, McLachlan AD, Pellegrini M, Bioinformatic challenges for the next decade(s), Philos Trans R Soc Lond B Biol Sci., 361(1467):525-7 (2006) PubMed Link PDF

2005

  1. Levskaya A, Chevalier AA, Tabor JJ, Simpson ZB, Lavery LA, Levy M, Davidson EA, Scouras A, Ellington AD, Marcotte EM, Voigt CA, Synthetic biology: Engineering Escherichia coli to see light, Nature, 438(7067):441-2 (2005) PubMed Link PDF the Science Daily press release Nature 2005 Gallery "First Glimpse" Nature feature on the iGEM competition featuring a bacterial portrait UT press release New York Times feature
  2. Ramakrishnan SR, Mao R, Nakorchevskiy AA, Prince JT, Willard WS, Xu W, Marcotte EM, Miranker DP, A fast coarse filtering method for protein identification by mass spectrometry, University of Texas Dept. of Computer Sciences, Technical Report, TR-05-06: (2005) PubMed PDF
  3. Wang R, Prince JT, Marcotte EM, Mass spectrometry of the M. smegmatis proteome: Protein expression levels correlate with function, operons, and codon bias, Genome Res., 15(8):1118-26 (2005) PubMed Link PDF
  4. Ramani AK, Bunescu RC, Mooney RJ, Marcotte EM, Consolidating the set of known human protein-protein interactions in preparation for large-scale mapping of the human interactome, Genome Biology, 6(5):R40 (2005) PubMed Link PDF
  5. Bunescu R, Ge R, Kate RJ, Marcotte EM, Mooney RJ, Ramani AK, Wong YW, Comparative experiments on learning information extractors for proteins and their interactions, Artif Intell Med., 33(2):139-55 (2005) PubMed Link PDF
  6. Ramani AK, Marcotte EM, Bunescu RC, Mooney RJ, Using biomedical literature mining to consolidate the set of known human protein-protein interactions, Intelligent Systems in Molecular Biology-ACL Workshop, : (2005) PubMed PDF
  7. Date SV, Marcotte EM, Protein function prediction using the Protein Link Explorer (PLEX), Bioinformatics, 21(10):2558-9 (2005) PubMed Link PDF Supplemental Web Site

2004

  1. Lee I, Date SV, Adai AT, Marcotte EM, A probabilistic functional network of yeast genes, Science, 306(5701):1555-8 (2004) PubMed PDF Supplemental methods Supplemental README Supplemental File 1 Supplemental File 2 Supplemental File 3 Supplemental File 4 Supplemental File 5 (Files 4 & 5 require a VRML viewer)
  2. Baliga NS, Bonneau R, Facciotti MT, Pan M, Glusman G, Deutsch EW, Shannon P, Chiu Y, Weng RS, Gan RR, Hung P, Date SV, Marcotte E, Hood L, Ng WV, Genome sequence of Haloarcula marismortui: a halophilic archaeon from the Dead Sea, Genome Res., 14(11):2221-34 (2004) PubMed PDF
  3. Fraser AG, Marcotte EM, Development through the eyes of functional genomics, Curr Opin Genet Dev., 14(4):336-42 (2004) PubMed Link PDF
  4. Bork P, Jensen LJ, Von Mering C, Ramani AK, Lee I, Marcotte EM, Protein interaction networks from yeast to human, Curr Opin Struct Biol, 14(3):292-9 (2004) PubMed Link PDF
  5. Adai AT, Date SV, Wieland S, Marcotte EM, LGL: Creating a map of protein function with an algorithm for visualizing very large biological networks, J Mol Biol, 340(1):179-90 (2004) PubMed Link PDF Supplemental Web Site Sourceforge Site For more recent support of LGL, see the LGL guide by Claire McWhite and the latest updates from the Opte Project
  6. Fraser AG, Marcotte EM, A probabilistic view of gene function, Nature Genetics, 36(6):559-64 (2004) PubMed Link PDF
  7. Marcotte EM, Practical computational approaches to infer protein function, Biosilico, 2:24-29 (2004) PubMed PDF
  8. Prince JT, Carlson MW, Wang R, Lu P, Marcotte EM, The need for a public proteomics repository, Nature Biotechnology, 22(4):471-472 (2004) PubMed Link Supplemental Web Site
  9. Date SV, Marcotte EM, Response to McDermott and Samudrala: Enhanced functional information from predicted protein networks, TRENDS in Biotechnology, 22(2):62-63 (2004) PubMed Link PDF

2003

  1. Dhillon IS, Marcotte EM, Roshan U, Diametrical clustering for identifying anti-correlated gene clusters, Bioinformatics, 19(13):1612-9 (2003) PubMed PDF
  2. Lu P, Nakorchevskiy A, Marcotte EM, Expression deconvolution: a reinterpretation of DNA microarray data reveals dynamic changes in cell populations, Proc Natl Acad Sci U S A, 100(18):10370-5 (2003) PubMed PDF Supplemental files (zipped folder containing executable .jar file, yeast test data and cell cycle basis vectors)
  3. Date SV, Marcotte EM, Discovery of uncharacterized cellular systems by genome-wide analysis of functional linkages, Nat Biotechnol., 21(9):1055-62 (2003) PubMed PDF Fig S1 Fig S2 Table S1
  4. Marcotte EM, Assembling a jigsaw puzzle with 20,000 parts, Genome Biol., 4(6):323 (2003) PubMed PDF
  5. Ramani AK, Marcotte EM, Exploiting the co-evolution of interacting proteins to discover interaction specificity, J Mol Biol., 327(1):273-84 (2003) PubMed PDF Supplemental Web Site
  6. Galagan JE, Calvo SE, Borkovich KA, Selker EU, Read ND, Jaffe D, FitzHugh W, Ma LJ, Smirnov S, Purcell S, Rehman B, Elkins T, Engels R, Wang S, Nielsen CB, Butler J, Endrizzi M, Qui D, Ianakiev P, Bell-Pedersen D, Nelson MA, Werner-Washburne M, Selitrennikoff CP, Kinsey JA, Braun EL, Zelter A, Schulte U, Kothe GO, Jedd G, Mewes W, Staben C, Marcotte E, Greenberg D, Roy A, Foley K, Naylor J, Stange-Thomann N, Barrett R, Gnerre S, Kamal M, Kamvysselis M, Mauceli E, Bielke C, Rudd S, Frishman D, Krystofova S, Rasmussen C, Metzenberg RL, Perkins DD, Kroken S, Cogoni C, Macino G, Catcheside D, Li W, Pratt RJ, Osmani SA, DeSouza CP, Glass L, Orbach MJ, Berglund JA, Voelker R, Yarden O, Plamann M, Seiler S, Dunlap J, Radford A, Aramayo R, Natvig DO, Alex LA, Mannhaupt G, Ebbole DJ, Freitag M, Paulsen I, Sachs MS, Lander ES, Nusbaum C, Birren B, The genome sequence of the filamentous fungus Neurospora crassa, Nature, 422(6934):859-68 (2003) PubMed PDF
  7. Bunescu R, Ge R, Kate R, Mooney R, Wong Y, Marcotte E, Ramani A, Learning to extract proteins and their interactions from Medline abstracts, ICML Workshop, : (2003) PubMed PDF

2002

  1. Mallick P, Marcotte EM, Making sense of proteomics: Using bioinformatics to discover a protein's structure, functions, and interactions, Proteins and Proteomics: A Laboratory Manual, Simpson RJ, ed., Cold Spring Harbor Press: (2002) PubMed
  2. Dhillon IS, Marcotte EM, Roshan U., Diametrical clustering for identifying anti-correlated gene clusters, The University of Texas at Austin, Department of Computer Sciences, Technical Report TR-02-49: (2002) PubMed PDF
  3. Marcotte EM, Predicting protein function and networks on genome-wide scale, Gene Regulation and Metabolism: Post-Genomic Computational Approaches, Collado-Vides J, Holfstadt R, eds., MIT press: (2002) PubMed PDF
  4. Verjovsky Marcotte CJ, Marcotte EM, Predicting functional linkages from gene fusions with confidence, Applied Bioinformatics, 1(2):1-8 (2002) PubMed PDF

2001

  1. Marcotte EM, Date SV, Exploiting big biology: Integrating large-scale biological data for functional inference, Brief Bioinform, 2(4):363-74 (2001) PubMed PDF
  2. Marcotte EM, The path not taken, Nature Biotechnology, 19(7):626-7 (2001) PubMed PDF
  3. Marcotte EM, Measuring the dynamics of the proteome, Genome Research, 11(2):191-3 (2001) PubMed PDF
  4. Marcotte EM, Xenarios I, Eisenberg D, Mining literature for protein interactions, Bioinformatics, 17(4):359-63 (2001) PubMed PDF README 500_abstracts_with_PMID Discriminating_words_for_interactions Discriminating_words_for_interactions_edited score_abstracts Perl script
  5. Eisenberg D, Marcotte E, Pellegrini M, Thompson M, Xenarios I, Yeates T, From genome sequences to protein interactions, FASEB J, 15:A724-A724 (2001) PubMed
  6. Xenarios I, Fernandez E, Salwinski L, Duan XJ, Thompson MJ, Marcotte EM, Eisenberg D, DIP: the database of interacting proteins: 2001 update, Nucleic Acids Res, 29(1):239-41 (2001) PubMed PDF

2000

  1. Eisenberg D, Marcotte EM, Xenarios I, Yeates TO, Protein function in the post-genomic era, Nature, 405(6788):823-6 (2000) PubMed Link PDF
  2. Marcotte EM, Xenarios I, van der Bliek A, Eisenberg D, Localizing proteins in the cell from their phylogenetic profiles, Proc Natl Acad Sci U S A., 97(22):12115-20 (2000) PubMed Link PDF
  3. Marcotte EM, Computational genetics: Finding function by non-homology methods, Curr Opin Struct Biol., 10(3):359-65 (2000) PubMed Link PDF
  4. Yang H, Fitz-Gibbon S, Marcotte EM, Tai JH, Hyman EC, Miller JH, Characterization of a thermostable DNA glycosylase specific for U/G and T/G mismatches from the hyperthermophilic archaeon Pyrobaculum aerophilum, J Bacteriol., 182(5):1272-9 (2000) PubMed Link PDF
  5. Thompson M, Marcotte E, Pellegrini M, Yeates T, Eisenberg D, Increasing the specificity of protein functional inference by the Rosetta Stone method, Currents in Computational Molecular Biology, Miyano S, Shamir R, Takagi T, eds., Universal Academy Press, Inc.: (2000) PubMed PDF
  6. Xenarios I, Rice DW, Salwinski L, Baron MK, Marcotte EM, Eisenberg D, DIP: the database of interacting proteins, Nucleic Acids Res., 28(1):289-91 (2000) PubMed Link PDF

1999

  1. Marcotte EM, Pellegrini M, Thompson MJ, Yeates TO, Eisenberg D, A combined algorithm for genome-wide prediction of protein function, Nature, 402(6757):83-6 (1999) PubMed Link PDF See also Sali, A. Genomics: Functional links between proteins. Nature 402, 23-26 (1999), Boston Globe (Nov. 3, 1999), Los Angeles Times (Nov. 4, 1999).
  2. Marcotte EM, Pellegrini M, Ng HL, Rice DW, Yeates TO, Eisenberg D, Detecting protein function and protein-protein interactions from genome sequences, Science, 285(5428):751-3 (1999) PubMed Link PDF See also Doolittle, R. F. Do you dig my groove? Nature: Genetics 23, 6-8 (1999).
  3. Marcotte EM, Pellegrini M, Yeates TO, Eisenberg D, A census of protein repeats, J Mol Biol., 293(1):151-60 (1999) PubMed Link PDF
  4. Pellegrini M, Marcotte EM, Thompson MJ, Eisenberg D, Yeates TO, Assigning protein functions by comparative genome analysis: protein phylogenetic profiles, Proc Natl Acad Sci U S A, 96(8):4285-8 (1999) PubMed Link PDF
  5. Pellegrini M, Marcotte EM, Yeates TO, A fast algorithm for genome-wide analysis of proteins with repeated sequences, Proteins: Struct. Funct. Genet., 35(4):440-6 (1999) PubMed Link PDF

1998

  1. Marcotte EM, Eisenberg D, Chicken prion tandem repeats form a stable, protease-resistant domain, Biochemistry, 38(2):667-76 (1998) PubMed Link PDF
  2. Cascio D, Goodwill K, Marcotte E, A look at the future of macromolecular structure determination, Rigaku J., 15:1-5 (1998) PubMed PDF
  3. Robertus JD, Monzingo AF, Marcotte EM, Hart PJ, Structural analysis shows five glycohydrolase families diverged from a common ancestor, J Exp Zool., 282(1-2):127-32 (1998) PubMed Link PDF

Pre - 1998

  1. Hollis T, Honda Y, Fukamizo T, Marcotte E, Day PJ, Robertus JD, Kinetic analysis of barley chitinase, Arch Biochem Biophys., 344(2):335-42 (1997) PubMed Link PDF
  2. Marcotte EM, Monzingo AF, Ernst SR, Brzezinski R, Robertus JD, X-ray structure of an anti-fungal chitosanase from Streptomyces N174, Nat Struct Biol., 3(2):155-62 (1996) PubMed PDF News & Views
  3. Monzingo AF, Marcotte EM, Hart PJ, Robertus JD, Chitinases, chitosanases, and lysozymes can be divided into procaryotic and eucaryotic families sharing a conserved core, Nat Struct Biol, 3(2):133-40 (1996) PubMed PDF
  4. Robertus, J. D., Hart, P. J., Monzingo, A. F., Marcotte, E. & Hollis, T, The structure of chitinases and prospects for structure-Based drug design, Can. J. Bot., 73 (Suppl. 1):S1142-S1146 (1995) PubMed PDF
  5. Kim YJ, Francisco L, Chen GC, Marcotte E, Chan CS, Control of cellular morphogenesis by the Ip12/Bem2 GTPase-activating protein: possible role of protein phosphorylation, J Cell Biol., 127(5):1381-94 (1994) PubMed Link PDF
  6. Marcotte E, Hart PJ, Boucher I, Brzezinski R, Robertus JD, Crystallization of a chitosanase from Streptomyces N174, J Mol Biol, 232(3):995-6 (1993) PubMed Link PDF

Patents

  1. WO2021236716A2 Methods, systems and kits for polypeptide processing and analysis. Priority to US18/056,970. Converted to PCT; published as WO2021236716A2 on November 25, 2021 and as WO2021236716A3 on June 23, 2022. US application filed November 18, 2022 and published as US 2024/0002925 A1 on January 4, 2024.
  2. # 63/153,285 Methods for polypeptide processing and analysis. PCT filed February 24, 2022 with serial number PCT/US2022/017642, published as US 2024/0125805 A1 on April 18, 2024. Chinese Patent Application published on 11/17/2023 under No. CN 117083391 A. European patent application published 1/3/2024 under Publication No. 4298235.
  3. # 63/193,328 Capture and analysis of proteins from single cells. PCT filed May 26, 2022 with serial number PCT/US2022/031022. US patent application US2024/0168034 A1 published as Methods and systems for single cell protein analysis May 23, 2024.
  4. # 63/193,436 Composition, methods and utility of conjugated biomolecule barcodes. PCT filed May 26, 2022 with serial number PCT/US22/31079. US patent application 2024/0201198 A1 published June 20, 2024.
  5. WO2022192661A1 Sars-cov-2 neutralizing antibodies and uses thereof . PCT filed March 11, 2022 and published as WO2022192661A1 on September 15, 2022.
  6. Publication # WO 2021236716 A2 Methods, systems and kits for polypeptide processing and analysis. PCT filed May 19, 2021.
  7. Publication # WO 2021168083 A1 Peptide and protein c-terminus labeling. Converted to PCT on 2/18/2021 with serial number PCT/US2021/018535. Japanese Patent Application published 4/5/2023 under Publication No. 2023-514316.
  8. Publication # WO 2020072907 A1 Solid-phase N-terminal peptide capture and release. PCT filed Oct 04, 2019.
  9. Publication # WO 2020037046 A1 Single molecule sequencing peptides bound to the major histocompatibility complex. PCT filed Aug 14, 2019. UK patent GB 2591384 B issued July 26, 2023. UK patent GB 2607829 B issued August 30, 2023.
  10. Publication # WO 2020023488 A1 Single molecule sequencing identification of post-translational modifications on proteins. PCT filed July 23, 2018.
  11. Publication # WO 2020014586 A1 Molecular neighborhood detection by oligonucleotides. PCT filed July 12, 2018.
  12. 10,175,249 B2, issued January 8, 2019. Proteomic identification of antibodies. Lavinder, Jason; Boutz, Danny; Wine, Yariv; Marcotte, Edward; Georgiou, George.
  13. 10,545,153 B2, issued January 28, 2020. Single molecule peptide sequencing. Publication # WO/2016/069124, Intl appl # PCT/US2015/050099, International filing date 15.09.2015. Marcotte, Edward; Anslyn, Eric; Ellington, Andrew; Swaminathan, Jagannath; Hernandez, Erik; Johnson, Amber; Boulgakov, Alexander; Bachman, Logan; Seifert, Helen. Improved single molecule sequencing. 11,162,952 B2, issued November 2, 2021. Canadian patent 2,961,493 issued October 3, 2023.
  14. 9,625,469, issued April, 18, 2017. Identifying peptides at the single molecule level. Marcotte, Edward; Swaminathan, Jagannath; Ellington, Andrew; Anslyn, Eric. Appl # 14128247, filed 22.06.2012; publication # US20140349860, 27.11.2014. UK patent GB2510499 issued April 8, 2020. 11,105,812 B2, issued August 31, 2021. Canadian patent CA 2,839,702 C issued April 20, 2021. US 11,435,358 B2, issued September 6, 2022. US application US 2023/0107647 A1 published April 6, 2023. German patent DE 112012002570T5 issued August 10, 2023.
  15. Publication # WO 2013067308 A2, Compositions and methods for inducing disruption of blood vasculature and for reducing angiogenesis, PCT filed Nov 2, 2012; provisional patent # 61/555,212 filed Nov 3, 2011.
  16. Publication # WO 2013055867 A1, Genes involved in stress response in plants, PCT filed Oct 11, 2012.
  17. USPTO Application # 20120215458, Orthologous phenotypes and non-obvious human disease models, PCT filed July 13, 2010; provisional patent # 61/225,427 filed July 14, 2009.
  18. 9,146,241, issued September 29, 2015. Proteomic identification of antibodies. Lavinder, Jason; Wine, Yariv; Boutz, Danny; Marcotte, Edward; Georgiou, George. Appl # 13/684,395, filed November 23, 2012.
  19. 9,090,674 B2, issued July 28, 2015. Rapid isolation of monoclonal antibodies from animals. Reddy, Sai; Ge, Xin; Lavinder, Jason; Boutz, Danny; Ellington, Andrew D.; Marcotte, Edward M.; Georgiou, George.
  20. 6,892,139, issued May 10, 2005. Determining the functions and interactions of proteins by comparative analysis.
  21. 6,772,069, issued August 3, 2004. Determining protein function and interaction from genome analysis.
  22. 6,564,151, issued May 13, 2003. Assigning protein functions by comparative genome analysis protein phylogenetic profiles.
  23. 6,466,874, issued October 15, 2002. Rosetta stone method for detecting protein function and protein-protein interactions from genome sequences.
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